I'm dealing with smallRNA Seq. My reads have UMI, which I extracted and appended to the read name using
extract. Then, I aligned using
bowtie and I got
.sam files for aligned reads.
I saw on
umi-tools manual that I should now collapse the reads using the
count_tab function, as I have bulk RNA-Seq (and a tool like
HTSeq is quite an overkill for miRNAs).
Anyway, I'm struggling with the command line I should use.
If I'm not wrong I should produce
.tsv files with columns [ read_name | miRNA aligned ] for each sample and sort the file by miRNA name. I tried with this input file, but it takes ages even if I pick the first 10 rows.
Does anybody have a guess about it?