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
467 stars 151 forks source link

Adapter Content after using TrimGalore #115

Closed NicMAlexandre closed 3 years ago

NicMAlexandre commented 3 years ago

I ran the following on paired-end RNASeq data:

TrimGalore-0.6.0/./trim_galore --paired --retain_unpaired --phred33 --output_dir trimmed_reads --length 36 -q 5 --stringency 1 -e 0.1 $1 $2

When looking at the fastqc report, I am still seeing adapter content. Are the above parameters correct?

image

NicMAlexandre commented 3 years ago

It looks like I may have used the wrong input file for the next step. Disregard.

FelixKrueger commented 3 years ago

excellent, I was just going through the CHANGELOG to see whether there was anything that might affect your processing (it might still be a good idea to upgrade to 0.6.6 if you have time...).

NicMAlexandre commented 3 years ago

Hi Felix,

Will do! My apologies.

On Tue, May 25, 2021 at 9:03 AM Felix Krueger @.***> wrote:

excellent, I was just going through the CHANGELOG to see whether there was anything that might affect your processing (it might still be a good idea to upgrade to 0.6.6 if you have time...).

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub https://github.com/FelixKrueger/TrimGalore/issues/115#issuecomment-847997326, or unsubscribe https://github.com/notifications/unsubscribe-auth/AFB6332YNOEGXX5QDQB4QQDTPPC3VANCNFSM45PVUS4A .

-- Best,

Nicolas Alexandre PhD Candidate, Integrative Biology Whiteman Lab University of California - Berkeley @. @.>