|Thread||Thread Starter||Forum||Replies||Last Post|
|Trimming adapters with Cutadapt||Elfangor||RNA Sequencing||3||08-10-2016 11:26 AM|
|cutadapt trimming for multiple files||lianov||Bioinformatics||13||11-14-2015 02:11 AM|
|Adapter trimming with cutadapt||Kulvait||Bioinformatics||3||05-05-2015 03:48 AM|
|3' trimming using cutadapt changes property of 5'.||Alex Lee||RNA Sequencing||0||04-17-2014 10:28 PM|
|Adapters trimming: Cutadapt vs Trimmomatic||MafaldaSF||Bioinformatics||8||03-20-2014 06:16 AM|
|04-21-2017, 04:41 AM||#1|
Join Date: May 2016
Cutadapt trimming issues
Hi, perhaps someone could advise me on the following issue.
I was trimming my paired-end reads with cut adapt using the following command:
cutadapt -a CTGTAGGCACCATCAATAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT --minimum-length 45 -o ~/Virus_S5_trimmed_min45_R1.fastq.gz -p ~/Virus_S5_trimmed_min45_R2.fastq.gz Virus_S5_R1.fastq.gz Virus_S5_R2.fastq.gz
This sequence is from one of the adaptors (I underlined it in the code), but I don't understand why does the cutadapt not trimm it off.
Any help would be appreciated.
|cutadapt, fastqc, trimming reads|