output explanation

[jianshu93]

Hello Ben,

I was doing some benchmark studies for dirseq (forward and reverse reads are used to map to genomes (30genomes put together)):

dirseq --bam ../all_mag_bwamem.filtered.bam --gff ../all_mag.gff --measure-type count

I have an example output from the above command:
try.txt

forward read count column is all reads (both forward and reverse reads) mapped to the gene strand right while reverse read count is all reads (both forward and reverse reads) mapped to the gene strand right, meaning this forward/reverse read count is referring to whether reads are mapped to gene strand (forward read count) or reverse strand of gene strand (reverse read count), but not forward reads or reverse reads right. Just to be clear. And if we have metaT reads, they should all map to the forward strand of gene strand, assuming stranded specific tool kit like Illumina TrueSeq and no DNA contamination?

Thanks,

Jianshu