command line for umi_tools count_tab

Question

[Luca]

Hi everyone,

I'm dealing with smallRNA Seq. My reads have UMI, which I extracted and appended to the read name using umi-tools's function 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?

[i.sudbery]

Can you show the command line you are using. It definitely shouldn't take ages with only ten rows.

Where is the miRNA id encoded in the alignment - is it in contig? (i.e. you've aligned to a fasta file of miRNA sequences). In this case you can use count instead of count_tab with the --per-contig option.