Hi,
I'm looking for single nucleotide variants (SNV) in my RNA-seq data. But after following bowtie mapping -> samtools mpileup -> bcftools pipeline; I see that it doesn't keep the directionality of the reads. It just take the reference and the alternate, ignoring if the mismatch is based on the forward or the reverse strand. So after looking at all the parameter that these programs can take into, I'm not able to find anything regarding this issue. The question seems pretty stupid and I'm feeling so because I can't find an answer for that; how to maintain the directionality in these case?
Thanks
I'm looking for single nucleotide variants (SNV) in my RNA-seq data. But after following bowtie mapping -> samtools mpileup -> bcftools pipeline; I see that it doesn't keep the directionality of the reads. It just take the reference and the alternate, ignoring if the mismatch is based on the forward or the reverse strand. So after looking at all the parameter that these programs can take into, I'm not able to find anything regarding this issue. The question seems pretty stupid and I'm feeling so because I can't find an answer for that; how to maintain the directionality in these case?
Thanks
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