Comments (4)
saketkc
commented on June 3, 2024
Hi @msbentsen
Thanks for the bug report. Your fix is perfect!
I am slowly moving away from using SRAmetadb.sqlite as it is not up-to-date. I would encourage you to try out the SRAweb mode which is automatically triggered if you do not have SRAmetadb.sqlite file in your current working directory (and you do not explicitly specify --db).
Here's an example in Google Colab for your project of interest: https://colab.research.google.com/drive/1Wmwv24dnLqlNFibn-0PuOtsJvXgpjbJ0
The SRAweb mode has clear advantages over the SRAmetadb.sqlite mode: resolves organism name, more structured metadata.
Output:
$ pysradb metadata SRP184142 --detailed
study_accession experiment_accession experiment_title experiment_desc organism_taxid organism_name library_strategy library_source library_selection sample_accession sample_title instrument total_spots total_size run_accession run_total_spots run_total_bases run_alias sra_url experiment_alias isolate host collection_date geo_loc_name tissue age number of animals in pool aliquot BioSampleModel sra_url_alt replicate sra_url_alt1 sra_url_alt2
SRP184142 SRX5345818 RNA-Seq of Exaiptasia pallida: adult RNA-Seq of Exaiptasia pallida: adult 1720309 Exaiptasia pallida RNA-Seq TRANSCRIPTOMIC RANDOM SRS4337592 N/A NextSeq 500 34640674 1076459911 SRR8543673 34640674 2757421989 apo_s2_24C.fastq https://sra-download.ncbi.nlm.nih.gov/traces/sra76/SRR/008343/SRR8543673 N/A missing not collected 2017-10-31 Israel whole animal adult 10 aliquot 2 Invertebrate N/A N/A N/A N/A
SRP184142 SRX5345817 RNA-Seq of Exaiptasia pallida: adult RNA-Seq of Exaiptasia pallida: adult 1720309 Exaiptasia pallida RNA-Seq TRANSCRIPTOMIC RANDOM SRS4337591 N/A NextSeq 500 32463900 1011013898 SRR8543674 32463900 2584023747 sym_s2_28C.fastq https://sra-download.ncbi.nlm.nih.gov/traces/sra76/SRR/008343/SRR8543674 N/A missing not collected 2017-10-31 Israel whole animal adult 10 aliquot 10 Invertebrate N/A N/A N/A N/A
SRP184142 SRX5345816 RNA-Seq of Exaiptasia pallida: adult RNA-Seq of Exaiptasia pallida: adult 1720309 Exaiptasia pallida RNA-Seq TRANSCRIPTOMIC RANDOM SRS4337590 N/A NextSeq 500 30819881 962783839 SRR8543675 30819881 2453392582 apo_s2_28C.fastq https://sra-download.ncbi.nlm.nih.gov/traces/sra76/SRR/008343/SRR8543675 N/A missing not collected 2017-10-31 Israel whole animal adult 10 aliquot 9 Invertebrate N/A N/A N/A N/A
SRP184142 SRX5345815 RNA-Seq of Exaiptasia pallida: adult RNA-Seq of Exaiptasia pallida: adult 1720309 Exaiptasia pallida RNA-Seq TRANSCRIPTOMIC RANDOM SRS4337589 N/A NextSeq 500 31955463 991848377 SRR8543676 31955463 2543650991 apo_s1_24C.fastq https://sra-download.ncbi.nlm.nih.gov/traces/sra76/SRR/008343/SRR8543676 N/A missing not collected 2017-10-22 Israel whole animal adult 10 aliquot 1 Invertebrate gs://sra-pub-src-3/SRR8543676/apo_s1_24C.fastq N/A N/A N/A
SRP184142 SRX5345814 RNA-Seq of Exaiptasia pallida: adult RNA-Seq of Exaiptasia pallida: adult 1720309 Exaiptasia pallida RNA-Seq TRANSCRIPTOMIC RANDOM SRS4337588 N/A NextSeq 500 29957604 928318673 SRR8543677 29957604 2384699540 sym_s3_34C.fastq https://sra-download.ncbi.nlm.nih.gov/traces/sra76/SRR/008343/SRR8543677 N/A missing not collected 2017-11-12 Israel whole animal adult 10 aliquot 12 Invertebrate N/A N/A N/A N/A
SRP184142 SRX5345813 RNA-Seq of Exaiptasia pallida: adult RNA-Seq of Exaiptasia pallida: adult 1720309 Exaiptasia pallida RNA-Seq TRANSCRIPTOMIC RANDOM SRS4337587 N/A NextSeq 500 28015324 876612694 SRR8543678 28015324 2229909683 apo_s3_34C.fastq https://sra-download.ncbi.nlm.nih.gov/traces/sra76/SRR/008343/SRR8543678 N/A missing not collected 2017-11-12 Israel whole animal adult 10 aliquot 11 Invertebrate s3://sra-pub-src-3/SRR8543678/apo_s3_34C.fastq N/A N/A N/A
SRP184142 SRX5345812 RNA-Seq of Exaiptasia pallida: adult RNA-Seq of Exaiptasia pallida: adult 1720309 Exaiptasia pallida RNA-Seq TRANSCRIPTOMIC RANDOM SRS4337585 N/A NextSeq 500 41548741 1289049550 SRR8543679 41548741 3307503282 sym_s4_34C.fastq https://sra-download.ncbi.nlm.nih.gov/traces/sra76/SRR/008343/SRR8543679 N/A missing not collected 2017-11-19 Israel whole animal adult 10 aliquot 14 Invertebrate N/A N/A N/A N/A
SRP184142 SRX5345811 RNA-Seq of Exaiptasia pallida: adult RNA-Seq of Exaiptasia pallida: adult 1720309 Exaiptasia pallida RNA-Seq TRANSCRIPTOMIC RANDOM SRS4337586 N/A NextSeq 500 37769073 1170287191 SRR8543680 37769073 3006696240 apo_s4_34C.fastq https://sra-download.ncbi.nlm.nih.gov/traces/sra76/SRR/008343/SRR8543680 N/A missing not collected 2017-11-19 Israel whole animal adult 10 aliquot 13 Invertebrate s3://sra-pub-src-3/SRR8543680/apo_s4_34C.fastq N/A N/A N/A
SRP184142 SRX5345810 RNA-Seq of Exaiptasia pallida: adult RNA-Seq of Exaiptasia pallida: adult 1720309 Exaiptasia pallida RNA-Seq TRANSCRIPTOMIC RANDOM SRS4337584 N/A NextSeq 500 35535878 1110824411 SRR8543681 35535878 2828562505 single_sym_s1_1_24C.fastq https://sra-download.ncbi.nlm.nih.gov/traces/sra76/SRR/008343/SRR8543681 N/A missing not collected 2017-10-22 Israel whole animal adult 10 aliquot 16 Invertebrate N/A N/A N/A N/A
SRP184142 SRX5345809 RNA-Seq of Exaiptasia pallida: adult RNA-Seq of Exaiptasia pallida: adult 1720309 Exaiptasia pallida RNA-Seq TRANSCRIPTOMIC RANDOM SRS4337583 N/A NextSeq 500 26204098 816715664 SRR8543682 26204098 2085594514 single_apo_s1_6_24C.fastq https://sra-download.ncbi.nlm.nih.gov/traces/sra76/SRR/008343/SRR8543682 N/A missing not collected 2017-10-22 Israel whole animal adult 10 aliquot 15 Invertebrate N/A N/A N/A N/A
SRP184142 SRX5345808 RNA-Seq of Exaiptasia pallida: adult RNA-Seq of Exaiptasia pallida: adult 1720309 Exaiptasia pallida RNA-Seq TRANSCRIPTOMIC RANDOM SRS4337582 N/A NextSeq 500 34621348 1079534006 SRR8543683 34621348 2755923808 sym_s2_24C.fastq https://sra-download.ncbi.nlm.nih.gov/traces/sra76/SRR/008343/SRR8543683 N/A missing not collected 2017-10-31 Israel whole animal adult 10 aliquot 6 Invertebrate s3://sra-pub-src-3/SRR8543683/sym_s2_24C.fastq N/A N/A N/A
SRP184142 SRX5345807 RNA-Seq of Exaiptasia pallida: adult RNA-Seq of Exaiptasia pallida: adult 1720309 Exaiptasia pallida RNA-Seq TRANSCRIPTOMIC RANDOM SRS4337581 N/A NextSeq 500 26265613 824474248 SRR8543684 26265613 2090496027 single_sym_s4_1_34C.fastq https://sra-download.ncbi.nlm.nih.gov/traces/sra76/SRR/008343/SRR8543684 N/A missing not collected 2017-11-19 Israel whole animal adult 10 aliquot 17 Invertebrate gs://sra-pub-src-3/SRR8543684/single_sym_s4_1_34C.fastq N/A N/A N/A
SRP184142 SRX5345806 RNA-Seq of Exaiptasia pallida: adult RNA-Seq of Exaiptasia pallida: adult 1720309 Exaiptasia pallida RNA-Seq TRANSCRIPTOMIC RANDOM SRS4337580 N/A NextSeq 500 39558198 1226815191 SRR8543685 39558198 3148875139 sym_s3_24C.fastq https://sra-download.ncbi.nlm.nih.gov/traces/sra76/SRR/008343/SRR8543685 N/A missing not collected 2017-11-12 Israel whole animal adult 10 aliquot 7 Invertebrate N/A N/A N/A N/A
SRP184142 SRX5345805 RNA-Seq of Exaiptasia pallida: adult RNA-Seq of Exaiptasia pallida: adult 1720309 Exaiptasia pallida RNA-Seq TRANSCRIPTOMIC RANDOM SRS4337579 N/A NextSeq 500 25289213 789199085 SRR8543686 25289213 2012736848 apo_s4_24C.fastq https://sra-download.ncbi.nlm.nih.gov/traces/sra76/SRR/008343/SRR8543686 N/A missing not collected 2017-11-19 Israel whole animal adult 10 aliquot 4 Invertebrate N/A N/A N/A N/A
SRP184142 SRX5345804 RNA-Seq of Exaiptasia pallida: adult RNA-Seq of Exaiptasia pallida: adult 1720309 Exaiptasia pallida RNA-Seq TRANSCRIPTOMIC RANDOM SRS4337578 N/A NextSeq 500 36980878 1144568902 SRR8543687 36980878 2943672084 apo_s3_24C.fastq https://sra-download.ncbi.nlm.nih.gov/traces/sra76/SRR/008343/SRR8543687 N/A missing not collected 2017-11-12 Israel whole animal adult 10 aliquot 3 Invertebrate N/A N/A N/A N/A
SRP184142 SRX5345803 RNA-Seq of Exaiptasia pallida: adult RNA-Seq of Exaiptasia pallida: adult 1720309 Exaiptasia pallida RNA-Seq TRANSCRIPTOMIC RANDOM SRS4337577 N/A NextSeq 500 27133954 849758475 SRR8543688 27133954 2160017844 sym_s4_24C.fastq https://sra-download.ncbi.nlm.nih.gov/traces/sra76/SRR/008343/SRR8543688 N/A missing not collected 2017-11-19 Israel whole animal adult 10 aliquot 8 Invertebrate N/A N/A N/A N/A
SRP184142 SRX5345802 RNA-Seq of Exaiptasia pallida: adult RNA-Seq of Exaiptasia pallida: adult 1720309 Exaiptasia pallida RNA-Seq TRANSCRIPTOMIC RANDOM SRS4337576 N/A NextSeq 500 38698712 1203697223 SRR8543689 38698712 3080505087 sym_s1_24C.fastq https://sra-download.ncbi.nlm.nih.gov/traces/sra76/SRR/008343/SRR8543689 N/A missing not collected 2017-10-22 Israel whole animal adult 10 aliquot 5 Invertebrate N/A N/A N/A N/A
SRP184142 SRX5338606 ATAC-Seq of Exaiptasia pallida: adult ATAC-Seq of Exaiptasia pallida: adult 1720309 Exaiptasia pallida ATAC-seq GENOMIC PCR SRS4331698 N/A Illumina HiSeq 2000 11442420 194593859 SRR8536103 11442420 583563420 stress_apo_34_s3_A.fastq https://sra-download.ncbi.nlm.nih.gov/traces/sra76/SRR/008336/SRR8536103 N/A missing not collected 2017-11-12 Israel whole animal adult N/A N/A Invertebrate N/A apo biological replicate 1 N/A N/A
SRP184142 SRX5338605 ATAC-Seq of Exaiptasia pallida: adult ATAC-Seq of Exaiptasia pallida: adult 1720309 Exaiptasia pallida ATAC-seq GENOMIC PCR SRS4331697 N/A Illumina HiSeq 2000 10411584 193183012 SRR8536104 10411584 530990784 control_apo_24_s2_F.fastq https://sra-download.ncbi.nlm.nih.gov/traces/sra76/SRR/008336/SRR8536104 N/A missing not collected 2017-10-31 Israel whole animal adult N/A N/A Invertebrate N/A apo biological replicate 2.3 N/A N/A
SRP184142 SRX5338604 ATAC-Seq of Exaiptasia pallida: adult ATAC-Seq of Exaiptasia pallida: adult 1720309 Exaiptasia pallida ATAC-seq GENOMIC PCR SRS4331696 N/A Illumina HiSeq 2000 16869690 266204029 SRR8536105 16869690 860354190 MS_apo_s2_28_F.fastq https://sra-download.ncbi.nlm.nih.gov/traces/sra76/SRR/008336/SRR8536105 N/A missing not collected 2017-10-31 Israel whole animal adult N/A N/A Invertebrate gs://sra-pub-src-3/SRR8536105/MS_apo_s2_28_F.fastq apo biological replicate 3 N/A N/A
SRP184142 SRX5338603 ATAC-Seq of Exaiptasia pallida: adult ATAC-Seq of Exaiptasia pallida: adult 1720309 Exaiptasia pallida ATAC-seq GENOMIC PCR SRS4331695 N/A Illumina HiSeq 2000 5728917 104791441 SRR8536106 5728917 292174767 MS_apo_s2_28_E.fastq https://sra-download.ncbi.nlm.nih.gov/traces/sra76/SRR/008336/SRR8536106 N/A missing not collected 2017-10-31 Israel whole animal adult N/A N/A Invertebrate N/A apo biological replicate 2 N/A N/A
SRP184142 SRX5338602 ATAC-Seq of Exaiptasia pallida: adult ATAC-Seq of Exaiptasia pallida: adult 1720309 Exaiptasia pallida ATAC-seq GENOMIC PCR SRS4331694 N/A Illumina HiSeq 2000 18597825 325835544 SRR8536107 18597825 948489075 control_apo_24_s2_E.fastq https://sra-download.ncbi.nlm.nih.gov/traces/sra76/SRR/008336/SRR8536107 N/A missing not collected 2017-10-31 Israel whole animal adult N/A N/A Invertebrate N/A apo biological replicate 2.2 N/A N/A
SRP184142 SRX5338601 ATAC-Seq of Exaiptasia pallida: adult ATAC-Seq of Exaiptasia pallida: adult 1720309 Exaiptasia pallida ATAC-seq GENOMIC PCR SRS4331693 N/A Illumina HiSeq 2000 5597040 94219434 SRR8536108 5597040 285449040 control_apo_24_s2_D.fastq https://sra-download.ncbi.nlm.nih.gov/traces/sra76/SRR/008336/SRR8536108 N/A missing not collected 2017-10-31 Israel whole animal adult N/A N/A Invertebrate N/A apo biological replicate 2.1 N/A N/A
SRP184142 SRX5338600 ATAC-Seq of Exaiptasia pallida: adult ATAC-Seq of Exaiptasia pallida: adult 1720309 Exaiptasia pallida ATAC-seq GENOMIC PCR SRS4331692 N/A Illumina HiSeq 2000 17226162 369910600 SRR8536109 17226162 878534262 control_apo_24_s1_B.fastq https://sra-download.ncbi.nlm.nih.gov/traces/sra76/SRR/008336/SRR8536109 N/A missing not collected 2017-10-22 Israel whole animal adult N/A N/A Invertebrate N/A apo biological replicate 2 N/A N/A
SRP184142 SRX5338599 ATAC-Seq of Exaiptasia pallida: adult ATAC-Seq of Exaiptasia pallida: adult 1720309 Exaiptasia pallida ATAC-seq GENOMIC PCR SRS4331691 N/A Illumina HiSeq 2000 8202111 139802599 SRR8536110 8202111 418307661 control_apo_24_s1_A.fastq https://sra-download.ncbi.nlm.nih.gov/traces/sra76/SRR/008336/SRR8536110 N/A missing not collected 2017-10-22 Israel whole animal adult N/A N/A Invertebrate N/A apo biological replicate 1 N/A N/A
SRP184142 SRX5338598 ATAC-Seq of Exaiptasia pallida: adult ATAC-Seq of Exaiptasia pallida: adult 1720309 Exaiptasia pallida ATAC-seq GENOMIC PCR SRS4331690 N/A Illumina HiSeq 2000 11856935 197103283 SRR8536111 11856935 604703685 MS_apo_28_s2_D.fastq https://sra-download.ncbi.nlm.nih.gov/traces/sra76/SRR/008336/SRR8536111 N/A missing not collected 2017-10-31 Israel whole animal adult N/A N/A Invertebrate N/A apo biological replicate 1 N/A N/A
SRP184142 SRX5338597 ATAC-Seq of Exaiptasia pallida: adult ATAC-Seq of Exaiptasia pallida: adult 1720309 Exaiptasia pallida ATAC-seq GENOMIC PCR SRS4331689 N/A Illumina HiSeq 2000 5004459 106259999 SRR8536112 5004459 255227409 control_apo_24_s1_C.fastq https://sra-download.ncbi.nlm.nih.gov/traces/sra76/SRR/008336/SRR8536112 N/A missing not collected 2017-10-22 Israel whole animal adult N/A N/A Invertebrate s3://sra-pub-src-3/SRR8536112/control_apo_24_s1_C.fastq apo biological replicate 3 N/A N/A
SRP184142 SRX5338596 ATAC-Seq of Exaiptasia pallida: adult ATAC-Seq of Exaiptasia pallida: adult 1720309 Exaiptasia pallida ATAC-seq GENOMIC PCR SRS4331688 N/A Illumina HiSeq 2000 21707955 442258199 SRR8536113 21707955 1107105705 control_sym_24_s4_B.fastq https://sra-download.ncbi.nlm.nih.gov/traces/sra76/SRR/008336/SRR8536113 N/A missing not collected 2017-11-19 Israel whole animal adult N/A N/A Invertebrate N/A sym biological replicate 4.1 N/A N/A
SRP184142 SRX5338595 ATAC-Seq of Exaiptasia pallida: adult ATAC-Seq of Exaiptasia pallida: adult 1720309 Exaiptasia pallida ATAC-seq GENOMIC PCR SRS4331687 N/A Illumina HiSeq 2000 25303884 485326454 SRR8536114 25303884 1290498084 control_sym_24_s4_E.fastq https://sra-download.ncbi.nlm.nih.gov/traces/sra76/SRR/008336/SRR8536114 N/A missing not collected 2017-11-19 Israel whole animal adult N/A N/A Invertebrate N/A sym biological replicate 4.2 N/A N/A
SRP184142 SRX5338594 ATAC-Seq of Exaiptasia pallida: adult ATAC-Seq of Exaiptasia pallida: adult 1720309 Exaiptasia pallida ATAC-seq GENOMIC PCR SRS4331686 N/A Illumina HiSeq 2000 61849885 1403480222 SRR8536115 61849885 3154344135 control_sym_24_s4_F.fastq https://sra-download.ncbi.nlm.nih.gov/traces/sra76/SRR/008336/SRR8536115 N/A missing not collected 2017-11-19 Israel whole animal adult N/A N/A Invertebrate N/A sym biological replicate 4.3 N/A N/A
SRP184142 SRX5338593 ATAC-Seq of Exaiptasia pallida: adult ATAC-Seq of Exaiptasia pallida: adult 1720309 Exaiptasia pallida ATAC-seq GENOMIC PCR SRS4331685 N/A Illumina HiSeq 2000 16869690 266204029 SRR8536116 16869690 860354190 MS_sym_28_s2_C.fastq https://sra-download.ncbi.nlm.nih.gov/traces/sra76/SRR/008336/SRR8536116 N/A missing not collected 2017-10-31 Israel whole animal adult N/A N/A Invertebrate N/A sym biological replicate 3 N/A N/A
SRP184142 SRX5338592 ATAC-Seq of Exaiptasia pallida: adult ATAC-Seq of Exaiptasia pallida: adult 1720309 Exaiptasia pallida ATAC-seq GENOMIC PCR SRS4331684 N/A Illumina HiSeq 2000 22118207 490024179 SRR8536117 22118207 1128028557 control_sym_24_s2_A.fastq https://sra-download.ncbi.nlm.nih.gov/traces/sra76/SRR/008336/SRR8536117 N/A missing not collected 2017-10-31 Israel whole animal adult N/A N/A Invertebrate N/A sym biological replicate 2.1 N/A N/A
SRP184142 SRX5338591 ATAC-Seq of Exaiptasia pallida: adult ATAC-Seq of Exaiptasia pallida: adult 1720309 Exaiptasia pallida ATAC-seq GENOMIC PCR SRS4331753 N/A Illumina HiSeq 2000 16869690 266204029 SRR8536118 16869690 860354190 MS_sym_28_s2_A.fastq https://sra-download.ncbi.nlm.nih.gov/traces/sra76/SRR/008336/SRR8536118 N/A missing not collected 2017-10-31 Israel whole animal adult N/A N/A Invertebrate N/A sym biological replicate 1 N/A N/A
SRP184142 SRX5338590 ATAC-Seq of Exaiptasia pallida: adult ATAC-Seq of Exaiptasia pallida: adult 1720309 Exaiptasia pallida ATAC-seq GENOMIC PCR SRS4331752 N/A Illumina HiSeq 2000 16869690 266204051 SRR8536119 16869690 860354190 MS_sym_28_s2_B.fastq https://sra-download.ncbi.nlm.nih.gov/traces/sra76/SRR/008336/SRR8536119 N/A missing not collected 2017-10-31 Israel whole animal adult N/A N/A Invertebrate N/A sym biological replicate 2 N/A N/A
SRP184142 SRX5338589 ATAC-Seq of Exaiptasia pallida: adult ATAC-Seq of Exaiptasia pallida: adult 1720309 Exaiptasia pallida ATAC-seq GENOMIC PCR SRS4331751 N/A Illumina HiSeq 2000 11367424 236197256 SRR8536120 11367424 579738624 control_sym_24_s1_E.fastq https://sra-download.ncbi.nlm.nih.gov/traces/sra76/SRR/008336/SRR8536120 N/A missing not collected 2017-10-22 Israel whole animal adult N/A N/A Invertebrate N/A sym biological replicate 2 N/A N/A
SRP184142 SRX5338588 ATAC-Seq of Exaiptasia pallida: adult ATAC-Seq of Exaiptasia pallida: adult 1720309 Exaiptasia pallida ATAC-seq GENOMIC PCR SRS4331750 N/A Illumina HiSeq 2000 11497118 236513389 SRR8536121 11497118 586353018 control_sym_24_s1_F.fastq https://sra-download.ncbi.nlm.nih.gov/traces/sra76/SRR/008336/SRR8536121 N/A missing not collected 2017-10-22 Israel whole animal adult N/A N/A Invertebrate N/A sym biological replicate 3 N/A N/A
SRP184142 SRX5338587 ATAC-Seq of Exaiptasia pallida: adult ATAC-Seq of Exaiptasia pallida: adult 1720309 Exaiptasia pallida ATAC-seq GENOMIC PCR SRS4331749 N/A Illumina HiSeq 2000 15289433 279245573 SRR8536122 15289433 779761083 control_apo_24_s4_F.fastq https://sra-download.ncbi.nlm.nih.gov/traces/sra76/SRR/008336/SRR8536122 N/A missing not collected 2017-11-19 Israel whole animal adult N/A N/A Invertebrate N/A apo biological replicate 4.3 N/A N/A
SRP184142 SRX5338586 ATAC-Seq of Exaiptasia pallida: adult ATAC-Seq of Exaiptasia pallida: adult 1720309 Exaiptasia pallida ATAC-seq GENOMIC PCR SRS4331748 N/A Illumina HiSeq 2000 25375005 563660312 SRR8536123 25375005 1294125255 control_sym_24_s1_D.fastq https://sra-download.ncbi.nlm.nih.gov/traces/sra76/SRR/008336/SRR8536123 N/A missing not collected 2017-10-22 Israel whole animal adult N/A N/A Invertebrate s3://sra-pub-src-3/SRR8536123/control_sym_24_s1_D.fastq sym biological replicate 1 N/A N/A
SRP184142 SRX5338585 ATAC-Seq of Exaiptasia pallida: adult ATAC-Seq of Exaiptasia pallida: adult 1720309 Exaiptasia pallida ATAC-seq GENOMIC PCR SRS4331747 N/A Illumina HiSeq 2000 18576644 423694963 SRR8536124 18576644 947408844 control_sym_24_s2_B.fastq https://sra-download.ncbi.nlm.nih.gov/traces/sra76/SRR/008336/SRR8536124 N/A missing not collected 2017-10-31 Israel whole animal adult N/A N/A Invertebrate s3://sra-pub-src-3/SRR8536124/control_sym_24_s2_B.fastq sym biological replicate 2.2 N/A N/A
SRP184142 SRX5338584 ATAC-Seq of Exaiptasia pallida: adult ATAC-Seq of Exaiptasia pallida: adult 1720309 Exaiptasia pallida ATAC-seq GENOMIC PCR SRS4331746 N/A Illumina HiSeq 2000 19738191 323267782 SRR8536125 19738191 1006647741 control_sym_24_s2_C.fastq https://sra-download.ncbi.nlm.nih.gov/traces/sra76/SRR/008336/SRR8536125 N/A missing not collected 2017-10-31 Israel whole animal adult N/A N/A Invertebrate N/A sym biological replicate 2.3 N/A N/A
SRP184142 SRX5338583 ATAC-Seq of Exaiptasia pallida: adult ATAC-Seq of Exaiptasia pallida: adult 1720309 Exaiptasia pallida ATAC-seq GENOMIC PCR SRS4331745 N/A Illumina HiSeq 2000 21843706 482631180 SRR8536126 21843706 1114029006 control_sym_24_s3_A.fastq https://sra-download.ncbi.nlm.nih.gov/traces/sra76/SRR/008336/SRR8536126 N/A missing not collected 2017-11-12 Israel whole animal adult N/A N/A Invertebrate s3://sra-pub-src-3/SRR8536126/control_sym_24_s3_A.fastq sym biological replicate 3.1 N/A N/A
SRP184142 SRX5338582 ATAC-Seq of Exaiptasia pallida: adult ATAC-Seq of Exaiptasia pallida: adult 1720309 Exaiptasia pallida ATAC-seq GENOMIC PCR SRS4331744 N/A Illumina HiSeq 2000 2067856 42761947 SRR8536127 2067856 105460656 stress_sym_34_s3_F.fastq https://sra-download.ncbi.nlm.nih.gov/traces/sra76/SRR/008336/SRR8536127 N/A missing not collected 2017-11-12 Israel whole animal adult N/A N/A Invertebrate N/A sym biological replicate 3 N/A N/A
SRP184142 SRX5338581 ATAC-Seq of Exaiptasia pallida: adult ATAC-Seq of Exaiptasia pallida: adult 1720309 Exaiptasia pallida ATAC-seq GENOMIC PCR SRS4331743 N/A Illumina HiSeq 2000 39970381 737110058 SRR8536128 39970381 2038489431 stress_sym_34_s4_E.fastq https://sra-download.ncbi.nlm.nih.gov/traces/sra76/SRR/008336/SRR8536128 N/A missing not collected 2017-11-19 Israel whole animal adult N/A N/A Invertebrate N/A sym biological replicate 3 N/A N/A
SRP184142 SRX5338580 ATAC-Seq of Exaiptasia pallida: adult ATAC-Seq of Exaiptasia pallida: adult 1720309 Exaiptasia pallida ATAC-seq GENOMIC PCR SRS4331764 N/A Illumina HiSeq 2000 81679335 1472607314 SRR8536129 81679335 4165646085 control_sym_24_s3_D.fastq https://sra-download.ncbi.nlm.nih.gov/traces/sra76/SRR/008336/SRR8536129 N/A missing not collected 2017-11-12 Israel whole animal adult N/A N/A Invertebrate s3://sra-pub-src-3/SRR8536129/control_sym_24_s3_D.fastq sym biological replicate 3.3 N/A N/A
SRP184142 SRX5338579 ATAC-Seq of Exaiptasia pallida: adult ATAC-Seq of Exaiptasia pallida: adult 1720309 Exaiptasia pallida ATAC-seq GENOMIC PCR SRS4331763 N/A Illumina HiSeq 2000 15291922 274201980 SRR8536130 15291922 779888022 control_sym_24_s3_C.fastq https://sra-download.ncbi.nlm.nih.gov/traces/sra76/SRR/008336/SRR8536130 N/A missing not collected 2017-11-12 Israel whole animal adult N/A N/A Invertebrate N/A sym biological replicate 3.2 N/A N/A
SRP184142 SRX5338578 ATAC-Seq of Exaiptasia pallida: adult ATAC-Seq of Exaiptasia pallida: adult 1720309 Exaiptasia pallida ATAC-seq GENOMIC PCR SRS4331762 N/A Illumina HiSeq 2000 8580565 155574147 SRR8536131 8580565 437608815 stress_sym_34_s4_D.fastq https://sra-download.ncbi.nlm.nih.gov/traces/sra76/SRR/008336/SRR8536131 N/A missing not collected 2017-11-19 Israel whole animal adult N/A N/A Invertebrate N/A sym biological replicate 2 N/A N/A
SRP184142 SRX5338577 ATAC-Seq of Exaiptasia pallida: adult ATAC-Seq of Exaiptasia pallida: adult 1720309 Exaiptasia pallida ATAC-seq GENOMIC PCR SRS4331761 N/A Illumina HiSeq 2000 5837718 130531547 SRR8536132 5837718 297723618 stress_sym_34_s4_C.fastq https://sra-download.ncbi.nlm.nih.gov/traces/sra76/SRR/008336/SRR8536132 N/A missing not collected 2017-11-19 Israel whole animal adult N/A N/A Invertebrate s3://sra-pub-src-3/SRR8536132/stress_sym_34_s4_C.fastq sym biological replicate 1 N/A N/A
SRP184142 SRX5338576 ATAC-Seq of Exaiptasia pallida: adult ATAC-Seq of Exaiptasia pallida: adult 1720309 Exaiptasia pallida ATAC-seq GENOMIC PCR SRS4331760 N/A Illumina HiSeq 2000 25223341 519179954 SRR8536133 25223341 1286390391 stress_sym_34_s3_B.fastq https://sra-download.ncbi.nlm.nih.gov/traces/sra76/SRR/008336/SRR8536133 N/A missing not collected 2017-11-12 Israel whole animal adult N/A N/A Invertebrate s3://sra-pub-src-3/SRR8536133/stress_sym_34_s3_B.fastq sym biological replicate 2 N/A N/A
SRP184142 SRX5338575 ATAC-Seq of Exaiptasia pallida: adult ATAC-Seq of Exaiptasia pallida: adult 1720309 Exaiptasia pallida ATAC-seq GENOMIC PCR SRS4331759 N/A Illumina HiSeq 2000 15866605 282527160 SRR8536134 15866605 809196855 stress_sym_34_s3_A.fastq https://sra-download.ncbi.nlm.nih.gov/traces/sra76/SRR/008336/SRR8536134 N/A missing not collected 2017-11-12 Israel whole animal adult N/A N/A Invertebrate N/A sym biological replicate 1 N/A N/A
SRP184142 SRX5338574 ATAC-Seq of Exaiptasia pallida: adult ATAC-Seq of Exaiptasia pallida: adult 1720309 Exaiptasia pallida ATAC-seq GENOMIC PCR SRS4331758 N/A Illumina HiSeq 2000 8158980 179439115 SRR8536135 8158980 416107980 control_apo_24_s4_C.fastq https://sra-download.ncbi.nlm.nih.gov/traces/sra76/SRR/008336/SRR8536135 N/A missing not collected 2017-11-19 Israel whole animal adult N/A N/A Invertebrate gs://sra-pub-src-3/SRR8536135/control_apo_24_s4_C.fastq apo biological replicate 4.2 N/A N/A
SRP184142 SRX5338573 ATAC-Seq of Exaiptasia pallida: adult ATAC-Seq of Exaiptasia pallida: adult 1720309 Exaiptasia pallida ATAC-seq GENOMIC PCR SRS4331757 N/A Illumina HiSeq 2000 22868175 509588303 SRR8536136 22868175 1166276925 control_apo_24_s4_B.fastq https://sra-download.ncbi.nlm.nih.gov/traces/sra76/SRR/008336/SRR8536136 N/A missing not collected 2017-11-19 Israel whole animal adult N/A N/A Invertebrate N/A apo biological replicate 4.1 N/A N/A
SRP184142 SRX5338572 ATAC-Seq of Exaiptasia pallida: adult ATAC-Seq of Exaiptasia pallida: adult 1720309 Exaiptasia pallida ATAC-seq GENOMIC PCR SRS4331683 N/A Illumina HiSeq 2000 21944102 417081757 SRR8536137 21944102 1119149202 stress_apo_34_s4_F.fastq https://sra-download.ncbi.nlm.nih.gov/traces/sra76/SRR/008336/SRR8536137 N/A missing not collected 2017-11-19 Israel whole animal adult N/A N/A Invertebrate N/A apo biological replicate 3 s3://sra-pub-src-3/SRR8536137/stress_apo_34_s4_F.fastq gs://sra-pub-src-3/SRR8536137/stress_apo_34_s4_F.fastq
SRP184142 SRX5338571 ATAC-Seq of Exaiptasia pallida: adult ATAC-Seq of Exaiptasia pallida: adult 1720309 Exaiptasia pallida ATAC-seq GENOMIC PCR SRS4331682 N/A Illumina HiSeq 2000 13522874 300909513 SRR8536138 13522874 689666574 stress_apo_34_s4_E.fastq https://sra-download.ncbi.nlm.nih.gov/traces/sra76/SRR/008336/SRR8536138 N/A missing not collected 2017-11-19 Israel whole animal adult N/A N/A Invertebrate N/A apo biological replicate 2 N/A N/A
SRP184142 SRX5338570 ATAC-Seq of Exaiptasia pallida: adult ATAC-Seq of Exaiptasia pallida: adult 1720309 Exaiptasia pallida ATAC-seq GENOMIC PCR SRS4331681 N/A Illumina HiSeq 2000 20462944 371292831 SRR8536139 20462944 1043610144 stress_apo_34_s4_D.fastq https://sra-download.ncbi.nlm.nih.gov/traces/sra76/SRR/008336/SRR8536139 N/A missing not collected 2017-11-19 Israel whole animal adult N/A N/A Invertebrate N/A apo biological replicate 1 N/A N/A
SRP184142 SRX5338569 ATAC-Seq of Exaiptasia pallida: adult ATAC-Seq of Exaiptasia pallida: adult 1720309 Exaiptasia pallida ATAC-seq GENOMIC PCR SRS4331680 N/A Illumina HiSeq 2000 41358948 712382402 SRR8536140 41358948 2109306348 control_apo_24_s3_E.fastq https://sra-download.ncbi.nlm.nih.gov/traces/sra76/SRR/008336/SRR8536140 N/A missing not collected 2017-11-12 Israel whole animal adult N/A N/A Invertebrate N/A apo biological replicate 3.3 N/A N/A
SRP184142 SRX5338568 ATAC-Seq of Exaiptasia pallida: adult ATAC-Seq of Exaiptasia pallida: adult 1720309 Exaiptasia pallida ATAC-seq GENOMIC PCR SRS4331679 N/A Illumina HiSeq 2000 6999125 112700345 SRR8536141 6999125 356955375 control_apo_24_s3_D.fastq https://sra-download.ncbi.nlm.nih.gov/traces/sra76/SRR/008336/SRR8536141 N/A missing not collected 2017-11-12 Israel whole animal adult N/A N/A Invertebrate N/A apo biological replicate 3.2 N/A N/A
SRP184142 SRX5338567 ATAC-Seq of Exaiptasia pallida: adult ATAC-Seq of Exaiptasia pallida: adult 1720309 Exaiptasia pallida ATAC-seq GENOMIC PCR SRS4331678 N/A Illumina HiSeq 2000 6987492 120942369 SRR8536142 6987492 356362092 control_apo_24_s3_A.fastq https://sra-download.ncbi.nlm.nih.gov/traces/sra76/SRR/008336/SRR8536142 N/A missing not collected 2017-11-12 Israel whole animal adult N/A N/A Invertebrate N/A apo biological replicate 3.1 N/A N/A
SRP184142 SRX5338566 ATAC-Seq of Exaiptasia pallida: adult ATAC-Seq of Exaiptasia pallida: adult 1720309 Exaiptasia pallida ATAC-seq GENOMIC PCR SRS4331677 N/A Illumina HiSeq 2000 16932864 302333495 SRR8536143 16932864 863576064 stress_apo_34_s3_C.fastq https://sra-download.ncbi.nlm.nih.gov/traces/sra76/SRR/008336/SRR8536143 N/A missing not collected 2017-11-12 Israel whole animal adult N/A N/A Invertebrate N/A apo biological replicate 3 N/A N/A
SRP184142 SRX5338565 ATAC-Seq of Exaiptasia pallida: adult ATAC-Seq of Exaiptasia pallida: adult 1720309 Exaiptasia pallida ATAC-seq GENOMIC PCR SRS4331676 N/A Illumina HiSeq 2000 2002699 38870622 SRR8536144 2002699 102137649 stress_apo_34_s3_B.fastq https://sra-download.ncbi.nlm.nih.gov/traces/sra76/SRR/008336/SRR8536144 N/A missing not collected 2017-11-12 Israel whole animal adult N/A N/A Invertebrate N/A apo biological replicate 2 N/A N/A
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msbentsen
commented on June 3, 2024
Hi @saketkc,
Thank you for the recommendation of the web mode - it works great!
I just have one follow up question - I see in the README.md that search is not available for SRAweb. Would it be a good idea to search in the SRAmetadb.sqlite for SRP's fitting to my keyword, and then use SRAweb to query the metadata for each SRP? Or is SRAmetadb.sqlite also not up-to-date in terms of available datasets?
Best Mette
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saketkc
commented on June 3, 2024
Hi @msbentsen, yes search doesn't work yet for SRAweb mode and it's going to take a while to have that functionality.
Meanwhile, you can use the search available through the SQLite mode. I have found out that SRAmetadb.sqlite misses out certain projects (SRP) or certain experiments (SRX) so searching on it might not give you a comprehensive result set. Some of the new datasets are definitely missing. Though, once you narrow down your list of SRPs, you can use the SRAweb mode to fetch its metadata.
Sorry, about the missing search option in the SRAweb mode. Unfortunately, I do not have control over the SRAmetadb.sqlite file creation, so I cannot comment on how updated it is. Hence, I am planning to completely do away with it.
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msbentsen
commented on June 3, 2024
Hi @saketkc,
Ah okay I see, it makes sense that you are planning to move away from it then. I still got plenty of hits with my query in the search on the sqlite database, so for my application it is not a big problem to lose a few. I think I will move forward with combined search in database + metadata from SRAweb. Thank you for your help!
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Related Issues (20)
- Filtering results by instrument type HOT 3
- [ENH] Super useful package!
- [BUG] cannot download a single experiment from command line HOT 1
- [BUG] aspera HOT 3
- [BUG] Metadata download not only for the provided accession number HOT 3
- [BUG] aspera HOT 3
- [BUG] gse-to-srp error HOT 1
- [BUG] Download error HOT 1
- [BUG] download error HOT 2
- [BUG]Downloading issue HOT 1
- fastq's URLs are empty HOT 2
- Not all attributes are being exported HOT 6
- [BUG] missing run-related entries for experiments with high number of runs
- [BUG] Metadata download only for a few run accessions, not for all the run accessions of the study HOT 4
- [BUG] srp-to-srr giving SRSs as result HOT 3
- could you expend to support European Nucleotide Archive data HOT 1
- [BUG] All arrays must be of the same length
- [ENH] geo_download_links error handling HOT 1
- Incosistencies with retrieving SRX data from different archives HOT 1
- Specific srp seems to cause metadata download to freeze
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