Hello all, I am doing some gene expression analysis. So I aligned my sequences with HISAT2 and now I am trying to run HTSeq to get read counts for each sample. Is it possible to run all samples together or we have to run it one by one? I was able to generate some data but there are few things that I do not understand. First when I open one of my files (see below) the first row for first column is empty and the second column has a weird number that I do not know where that comes from (I thought that the first column should be your genes ID and second column should be reads number with your sample ID but the sample ID seems missing? My sequence was paired end and here is the command that I used for HTseq

htseq-count 68A.sam  genome.gtf --stranded=no > 68A_htseq_counts.txt
    65996
LOC112214177    2
LOC112214178    0
LOC112214179    1748
LOC112214180    2113
LOC112214181    1
LOC112214182    0
LOC