cut adapter using trim galore
Hi,
can anyone help me how to trim adapter for multiple fastq files using trim galore. I have like 100 files paired end which are something like "W-CA-019-2-19_S6_LAll_R1_001.fastq.gz X-CA-022-2-20_S2_LAll_R1_001.fastq.gz W-CA-019-2-19_S6_LAll_R2_001.fastq.gz X-CA-022-2-20_S2_LAll_R2_001.fastq.gz". thanks in advance.
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Discrepancies in Sequence Length Distribution Between Trim Galore and Trimmomatic During Adapter Tr…
written by George •
-
invalid deflate data (invalid code lengths set)
written by leonmcswain •
-
It is weird there are no reads less than 100 bp in qualimap.
written by Dan •
-
snakemake wildcard for fastq files
written by arshil •
-
How to speed up trimming using trim galorer
written by lamia_203
-
problem with bowtie2 allignment
written by arshil •
-
Trim_galore on multiple fast.qz files: syntax problem
written by m98
-
Cutadapt for paired end RRBS data
written by anikb •
-
Trim Galore Bug?
written by datascientist28
-
tophat-fusion for gene fusion detection
written by Jackie
This thread shows how to use parallel with TrimGallore: TrimGalore! on multiple paired fastq files
There are many, many other threads with loop examples, you may read them to get started:
Bash Script Loop Help
For loop script
cutadapt loop and paired-end reads
bash loop for alignment RNA-seq data
Hello khandaud15!
Questions similar to yours can already be found at:
We have closed your question to allow us to keep similar content in the same thread.
If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.
Cheers!