hello, Cao! Thanks to your great work! I met an problem that which is paritag.sam in 2.construct_hicFiles_for_rRNA? There is no pairtag.sam in the result of step1! Looking forward to your reply!

Hi,
The RIC-seq is a wonderful method to explore the RNA-RNA interactions. I believe an important role it will play in the future.
After download your article data and analyze it, I noticed an output of STAR by using:

STAR --runMode alignReads \
--genomeDir $index \
--readFilesIn "$i".gz \
--readFilesCommand zcat \
--runThreadN 20 \
--outFileNamePrefix "$i". --outFilterMultimapNmax 100 --outSAMattributes All --alignIntronMin 1 \
--scoreGapNoncan -4 --scoreGapATAC -4 --chimSegmentMin 15 --chimJunctionOverhangMin 15 \
--alignSJoverhangMin 15 --alignSJDBoverhangMin 10 --alignSJstitchMismatchNmax 5 -1 5 5

which output a SRR8632821_1.Chimeric.out.junction rather than the YourSample_read1_toGenomeChimeric.out.sam decribed in your RIC-seq/1.find_pairTags_from_STAR_results/work.sh.

I tried use :

perl 1.find_pairTags_from_STAR_results/precess_Chimeric_sam.pl SRR8632821_1.Chimeric.out.junction > SRR8632821_1.Chimeric.out.junction.sam

But get nothing.

It's there some wrong in my code? Or where need I modify it ?

Thanks in advance for your reply.

Best wishes

Haifeng Sun
NanJing Medical University
2020.06.29

I read the paper "RIC-seq for global in situ profiling of RNA–RNA spatial interactions", and I want to see the RNA interaction. But I just can download the .hic file. I have no idea to chage the .hic file to a readable file.

If you can provide the chimeric reads infomation in readable way, I will really apreciate.

Hi,
RIC-seq technology is a helpful method to profile global RNA-RNA interactions, and I am very interested in the results showing published paper. So I downloaded RIC-seq data from the GEO database and tried the downstream analysis.
I have trimmed adapters and PCR duplicates as paper described, but confused about the steps about clipping the poly(N) tails. I noticed the software cutadapt, but about the parameter settings, could you give me some suggestions?
Thanks in advance!

Best wishes
Qianzhao

Hi,
I have downloaded RIC-seq data from the GEO database and tried the downstream analysis as described in your github.
I have successfully finished step1 find_pairTags_from_STAR_results and got interaction Samfiles, but when I tried to convert the Samfiles to hicFiles using the scripts in 2.construct_hicFiles_for_rRNA :

perl $RIC/sam_to_loops.pl $sam chr1 0 100000000 > $result/chr1_loops.txt &&
perl $RIC/interaction_from_loop_to_JuiceBox.pl $result/chr1_loops.txt > $result/chr1_loops.list &&
cat $result/chr1_loops.list | sort -k3,3 -k7,7 > $result/chr1_loops.sorted.list &&
java -jar $juice pre -r 1,2,5,10,20,50 $result/chr1_loops.sorted.list $result/${sample}.chr1.RR.hic $chr1_size &&

Finally, I got a very small hicFiles (just only a few kb) and I can't open it in juicebox. There is the warnings from juicertools:

WARN [2021-01-05T02:55:16,293] [Globals.java:138] [main] Development mode is enabled
Not including fragment map
Start preprocess
Writing header
Writing body
.java.lang.IllegalArgumentException: Illegal initial capacity: -1809845095
at java.util.HashMap.(HashMap.java:448)
at java.util.HashMap.(HashMap.java:467)
at java.util.LinkedHashMap.(LinkedHashMap.java:359)
at juicebox.tools.utils.original.Preprocessor$MatrixZoomDataPP.(Preprocessor.java:1578)
at juicebox.tools.utils.original.Preprocessor$MatrixPP.(Preprocessor.java:1450)
at juicebox.tools.utils.original.Preprocessor.writeBody(Preprocessor.java:765)
at juicebox.tools.utils.original.Preprocessor.preprocess(Preprocessor.java:419)
at juicebox.tools.clt.old.PreProcessing.run(PreProcessing.java:121)
at juicebox.tools.HiCTools.main(HiCTools.java:96)

and my juicertools version is juicer_tools_1.13.02.jar.

I don't know what happened, Could you give me some advice?

Here is the small hicFile:
chr1.zip
Here is the looplist file:
chr1_loops.zip

Thanks in advance!

Bests,
Qianzhao