TrimGalore

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trimgalore and cutadapt in two steps?

6

Hi team I know that trimgalore is a wrapper around cutadapt but I want to check what I ran is considered fine I ran trimgalore to remove adaptors and primers...

marwa38

Using TrimGalore for different rounds of adaptor cuttings

4

Hi! I am trying to implement the following _cutadapt_ command using TrimGalore: ``` cutadapt -m 20 -O 20 -a "polyA=A{20}" -a "QUALITY=G{20}" -n 2 fastq_extracted/sample/R1.fastq.gz | cutadapt -m 20 -O...

carmencita

Can trimgalore be used to clean up mate pair libraries?

3

Wondering if trimgalore can be used to cleanup mate-paired libraries? Is yes, is there a specific flag(s)?

gunjanpandey

(new) problem with output having reads that don't have a mate in R1 and R2 files.

2

Hello, I used trim-galore last year to clean up a lot of fastq.gz files I received from my service provider. It worked great and I was able to use the...

bmillerlab

Adapter trimming in RRBS

13

Hi Felix, We've recently analysed a paired-end 150 bp RRBS dataset, which ended having insert sizes well below 100 bp. This really concerned us, because insert size is having a...

franrodalg

Adapter Trimming on PE reads have different number of reads output

1

Hello, trim_galore -o output --fastqc --paired $R1_file $R2_file I have utilized trim-galore to trim illumina adapters on my PE sequencing reads. When I tried to process the output fq files...

bshim181

It seems like a good idea to pass on additional parameters to Cutadapt, e.g. `--poly-a`. In the current form, this can only be done via the `-a "SEQUENCE --additional_param" workaround,...

FelixKrueger

High PolyA content in R2 reads after trimming.

3

Hello I am working with human whole-genome bisulfite sequencing data, and paired-end reads. After using Trim Galore to remove adapters, I encountered an issue with the FastQC report for R2...

AmrSaadeldin

problems installing via conda/mamba

1

Relatively new to everything that isn't Windows I'm afraid.. can anyone help me out here? ``` (kraken2) martin@martin-VirtualBox:~$ mamba install -c bioconda trim-galore Looking for: ['trim-galore'] bioconda/linux-64 Using cache bioconda/noarch...

mawa86

Trim galore gets stuck on quality and adapter trimming

3

Hey, I am trying to trim pacbio sequencing data in a fastq file using trim galore. However, in every run trim galore gets stuck on the trimming step and never...

aman-akash