Hi,
I want to get the read counts for gene expression analysis. I used "samtools idxstats <bam file>" and got the four columns of "contig ID, read length, #mapped reads and # unmapped reads".
My question is I should use #mapped reads(the third column) or (#mapped reads + # unmapped reads)/2 as the raw reads count?
Thank you in advance!
Victoria
I want to get the read counts for gene expression analysis. I used "samtools idxstats <bam file>" and got the four columns of "contig ID, read length, #mapped reads and # unmapped reads".
My question is I should use #mapped reads(the third column) or (#mapped reads + # unmapped reads)/2 as the raw reads count?
Thank you in advance!
Victoria
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