Hi,
Can someone let me know if there is a need of filtering variants based on strand bias (SP tag of samtools) for a strand specific RNAseq data? I am trying to understand its concept specifically for strand specific RNAseq data for which I haven't got any document.
Near each end of a transcript you'll always get a bias, so ignore it there. If you are using paired-end reads, then you shouldn't see as much bias in the middle of transcripts and there perhaps filtering makes sense.
Thanks for your quick reply. I am using paired-end reads. Currently in some on my analyses I have included variants where SP <= 60 (based on some literatures). Unfortunately, I am unable to understand how SP in samtools is calculated and would like to know that as well just to be sure if I have chosen the right filtering parameter.
Thanks..is it same is this? https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_gatk_tools_walkers_annotator_FisherStrand.php
I was wondering if SP and FS (from GATK) are calculated in the same manner.
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version 2.3.6
I'd carefully evaluate strand bias filtering on your RNA-seq data before using it. It should never be used on single-end strand-specific libraries, but even on paired-end libraries I speculate you'd get a lot of bias due to short and partially-digested transcripts.
Hi,
Could you kindly let me know why it should not be used in single end strand specific library?
Because then everything SHOULD show strand bias.
I was giving it a thought and was just going to write it..you replied before..hehe..but yes.. according to my understanding, there won't be any reads arising from the opposite strand ( based on which strand is chosen for sequencing based on needs)..thanks anyway.. correct me if I am wrong..