The order of inclusion and exclusion transcript is reversed for the mutually exclusive events yielded by eventGenerator in the ioe file to the one generated directly using SUPPA.

Dear Team,
I read through the paper and found your tool, yanagi, very powerful and I'm excited to try it.

This is just a question rather than issue. I have an RNA-Seq dataset with the following characteristics:

1. paired-end
2. Unstranded
3. polyA+
4. read length : 75 bp
5. library depth: ranging from 23 to 33M reads (fragment) per library.
6. My RNA-seq is performed in 2 conditions (silencing vs control) in triplicate each.

My interest is to study alternative splicing changes upon the silencing experiment. In theory I want to check for SE, MXE, A5SS, A3SS, AF, AL, and diffrential polyadenylation site usage.

Can I apply yanagi on my dataset?

Thank you so much in advance!
Kind regards,
Jamal.

Dear Team,

While tying to run yanagi on .fastq.gz read files, I got the following error:
index:
unmated read(s): /home/jelhasnaoui/ref/OriginalData/DeBortoli/03_2016_RNASeq_Noncoding/Sample_LNA_CTRL_1_R1.fastq.gz
output:
num. threads: 1
max num. hits: 200
quasi-coverage: 0
no output: false
sensitive: true
strict check: true
fuzzy intersection: false
do chaining : false
selective alignment: false
no orphans: false
no dovetail: false

terminate called after throwing an instance of 'cereal::RapidJSONException'
what(): rapidjson internal assertion failure: IsObject()
[2020-03-04 00:01:40.050] [stderrLog] [warning]

NOTE: It appears you are running rapmap without the selective-alignment (--selAln) option.
Selective alignment can generally improve both the sensitivity and specificity of mapping,
with only a moderate increase in use of computational resources.
Unless there is a specific reason to do this (e.g. testing on clean simulated data),
--selAln is generally recommended.

[2020-03-04 00:01:40.050] [stderrLog] [info]
command line options

index:
unmated read(s): /home/jelhasnaoui/ref/OriginalData/DeBortoli/03_2016_RNASeq_Noncoding/Sample_LNA_CTRL_1_R2.fastq.gz
output:
num. threads: 1
max num. hits: 200
quasi-coverage: 0
no output: false
sensitive: true
strict check: true
fuzzy intersection: false
do chaining : false
selective alignment: false
no orphans: false
no dovetail: false

terminate called after throwing an instance of 'cereal::RapidJSONException'
what(): rapidjson internal assertion failure: IsObject()
Done
Elapsed Time: 0.4534430503845215
Done
Elapsed Time: 0.4746520519256592
Processing Alignments...
Mapped Reads: 0 Unmapped Reads: 0 Unmapped Due Txs: 0 Unmapped Due Direction: 0
Done!
Elapsed Time: 0.00027108192443847656
Writing Segments Counts...
Error
Traceback (most recent call last):
File "yanagi.py", line 62, in main
alignSegments.main()
File "/vol1/Analysis/DeBortoli/RNASeq_Noncoding_LNA_siRNA/yanagi-0.1/segmentsAligner.py", line 29, in main
alignAndCount(args.segs_ref_file, args.output_file, args.align_command1, args.align_command2)
File "/vol1/Analysis/DeBortoli/RNASeq_Noncoding_LNA_siRNA/yanagi-0.1/lib/SegCounter.py", line 265, in alignAndCount
writeSegPairCounts(outf, segPairs_counts, newsegPairs_counts, segPairs_txs, segsDict)
File "/vol1/Analysis/DeBortoli/RNASeq_Noncoding_LNA_siRNA/yanagi-0.1/lib/SegCounter.py", line 29, in writeSegPairCounts
for segPair in sorted(segPairs_counts.iterkeys()):
AttributeError: 'Counter' object has no attribute 'iterkeys'

Should I change the read file from .fastq.gz file to ".fa" format?
Can I also run RapMap using "--selAln" option?

Thank you!
Kind regards,
Jamal.

Good afternoon!
I am interested in using Yanagi tool, but I am not sure if the tool is suitable for my data
I have a paired-end RNA-seq, the forward read length is 100bp but the reverse read length is 66bp. since the -L option is critical for the quality of the results, I am not sure if the tool is suitable for my case. If it is, which value should I choose?