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
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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 @. @.>