max length in cutadapt

Question

[max_19]

Hi all! I'm trying to remove adapter sequences from my RNA-seq dataset, and i am only interested in reads that are 20-30bp in length. So I used cutadapt with the following specifications:

cutadapt -a $adapter -m 20 -M 30

In the cutadapt user guide, it states that

--maximum-length LENGTH or -M LENGTH Discard processed reads that are longer than LENGTH. Reads that are too long even before adapter removal are also discarded.

my raw reads are all 50bp, so they are already longer than my specified M value (30). Does this mean that cutadapt will get rid of all my reads?

When I run cutadapt though, I still get a good # of reads left over (e.g. 80-90%), so i'm not sure if I understand this M parameter incorrectly.

Thanks for the input guys,

Answer 1

[Devon Ryan]

"processed reads" are what's left after trimming but before filtering for length. Since you have a sRNA prep most of the reads will get trimmed and likely be below 30 bases thereafter (thus being under the maximum length).

[max_19]

That makes sense, thank you. I think the part that confuses me is the "Reads that are too long even before adapter removal are also discarded."

[Devon Ryan]

The documentation is wrong there.