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unmapped reads in fastq/fasta format and pair-end data #32
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Hi Yiwei, You are right that STAR produces partially-mapped reads, which are potentially T or B receptor reads. I would recommend saving the bam file with both mapped and unmapped reads. You can consider using our script for STAR with tuned parameters which will produce BAM file with both mapped and unmapped reads : https://github.com/smangul1/recycle.RNA.seq/blob/master/benchmark_RNASeq_aligners/code/run.STAR.tuned.sh Please let me know if it works. Serghei |
Hi, Serghei. Thank you for your quick reply! Sorry I didn't make myself clear. I've already done the alignment using To my understanding,
So the first case doesn't suit me, I have to follow the second. And my questions are:
Thank you for your help! Bests, |
Hi Yiwei, Please merge PE into one file. Also to use --digGold, you need to provide original reads, not the unmapped reads. Please let me know how it goes. If this doesn't' work for you, we can implement the option to allow to supply bam with mapped and FASTQ with unmapped (this is on our TODO list anyway). Thanks, Serghei |
OK! Thank you for your help! Also looking forward to the new version of BTW, the link https://github.com/smangul1/Profiling-adaptive-immune-repertoires-across-multiple-humantissues-by-RNA-Sequencing.ImRePconsistentlyoutperformedexistingmethods in your paper is broken. |
Hello,
I want to try
imrep
with my RNA-seq data. I've aligned thefastq
to genome withSTAR
, and saved the unmapped reads infastq
format (using--outReadsUnmapped Fastx
). As you said,STAR
produces partially-mapped reads. In such case, can I feedimrep
with theBAM
file together with unmappedfastq
?And another question, it seems
imrep
only accepts singlefastq
file as input when user want to use--digGold
and-a
options. Should I justcat
twofastq
? Orimrep
just works for single-end data in such case?Thanks!
Yiwei Niu
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