search

FelixKrueger / TrimGalore

A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data
GNU General Public License v3.0
461 stars 150 forks source link

Disabling adapter removal process while running #51

Closed EgeDede562 closed 5 years ago

EgeDede562 commented 5 years ago

Dear Felix,

I am trying to do a quality trimming with trimgalore with fastq files that have already had their adaptor sequences removed and unfortunately I do not have access to the original files. When I run trimgalore however it autodetects the illumina adaptor and tries to remove it. Is there any way of disabling this step? or should I just increase my specificity parameter to 13-14? (as it was 1, I clipped a lot of reads by accident).

Thank you

FelixKrueger commented 5 years ago

You could just select an adapter sequence that doesn't exist, e.g. -a X. That way, no adapter sequence should be clipped. Cheers, Felix