command line for umi_tools count_tab
Entering edit mode
15 days ago
Luca • 0

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?

umi-tools • 132 views
Entering edit mode

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.


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