m option in cutadapt

Question

[zizigolu]

Sorry guys,

In $CUT/cutadapt -a CTGTAGGCACCATCAAT filename.fastq > fielename_trimmed.fastq syntax

Which should I add to exclude the reads with less than 15 bases? I mean m option about which I could not find any clue in cutadapt documentation

Answer 1

[Asaf]

From cutadapt -h:

-m LENGTH, --minimum-length=LENGTH
                        Discard trimmed reads that are shorter than LENGTH.
                        Reads that are too short even before adapter removal
                        are also discarded. In colorspace, an initial primer
                        is not counted (default: 0).

So you should add -m 15

[zizigolu]

Thank you Asaf

[xiaoleiusc]

Is the -m from cutadapt setting minimal length before adaptor trimming or after adapter trimming?