FelixKrueger TrimGalore issues

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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issues

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trimgalore and cutadapt in two steps?

#147 marwa38 opened 2 years ago
6
Can trimgalore be used to clean up mate pair libraries?

#146 gunjanpandey opened 2 years ago
3
Update Ovation RRBS kit info

#145 michael-weinstein closed 2 years ago
0
Fixes CPU warning bounds

#144 sclamons closed 2 years ago
0
(new) problem with output having reads that don't have a mate in R1 and R2 files.

#143 bmillerlab closed 9 months ago
3
Can anyone explain Why in default mode -- paired --retain_unpaired only read2 read are retain and not read1

#142 veeramv closed 2 years ago
5
cutadapt: error: unrecognized arguments: -f P2_A01_M_0001.fastq Cutadapt terminated with exit signal: '512'.

#141 sevmurdock closed 2 years ago
4
Segmentation fault when disk space is low

#140 pinin4fjords closed 2 years ago
3
Run TrimGalore on a FASTA input

#139 vkkodali closed 2 years ago
1
equivalent of `--discard-untrimmed` parameter in `trim_galore`

#138 bounlu closed 2 years ago
1
`--max_n` value as a fraction

#137 bounlu closed 2 years ago
4
After trimming 10 bp at 5', the GC content at 3' changed oddly

#136 XiaoTW123 closed 2 years ago
3
TrimGalored sequence cannot be mapped with Bowtie2

#135 moqri closed 2 years ago
2
Changelog doesn't mention 0.6.7

#134 HenrikBengtsson closed 2 years ago
1
How is an error defined?

#133 CharlotteAnne closed 2 years ago
2
Adapter trimming in RRBS

#132 franrodalg opened 2 years ago
13
Trim-galore fails at quality check for some samples but not others

#131 bonzay36 closed 2 years ago
3
adapter+quality trimming followed by hard-trimming

#130 pmenzel closed 2 years ago
5
No reads end with "A" after trimming

#129 hkaspersen closed 2 years ago
2
cutadapt: error: unrecognized arguments: -f

#128 samsharr closed 2 years ago
4
Does TrimGalore handle the Illumina T-overhang

#127 pcantalupo closed 2 years ago
20
How to properly specify a basename?

#126 jolespin closed 2 years ago
2
The --nextseq argument doesn't change the parameters of cutadapt

#125 josephhughes closed 3 years ago
3
Cutadapt version error

#124 Jacob-Ferrier closed 2 years ago
3
cutadapt cores option docs are misleading

#123 keiranmraine closed 3 years ago
1
FastQC location as argument to trim_galore

#122 niekwit closed 3 years ago
2
primerset?

#121 marwa38 closed 3 years ago
2
Adapter trimming of Illumina DNA PCR-Free prep sequences

#120 andrews-matt closed 3 years ago
3
Incomplete trimming of Illumina adapters

#119 ag1805x closed 3 years ago
3
SOLiD sequencing data processing

#118 dahun73 closed 3 years ago
2
cutadapt: error: [Errno 2] No such file or directory: 'file.fastq\xa0'

#117 Hannah1746 closed 3 years ago
2
Multicore support not enabled

#116 dahun73 closed 3 years ago
1
Adapter Content after using TrimGalore

#115 NicMAlexandre closed 3 years ago
3
Update Trim_Galore_User_Guide.md

#114 eafyounian closed 3 years ago
1
The report is ok but fastqc result shows trimming process hasn't been done

#113 xjs1996 closed 3 years ago
4
FastQC fails after trimming due to "No such file or directory..."

#112 kubu4 closed 3 years ago
2
Adapter sequence must contain DNA characters only (A,C,T,G or N)!

#111 titand98 closed 3 years ago
2
Error - adapter trimming

#110 bioramg closed 2 years ago
12
Incompatibility error with latest python 3.9.0

#109 janstrauss1 closed 4 years ago
2
TrimGalore removes overrepresented sequences only from R2, R1 untouched.

#108 kvn95ss closed 4 years ago
3
Question about auto detected adapter sequnces and trimming only 3' or 5' end

#107 dahun73 closed 3 years ago
2
input file

#106 YspCoder closed 4 years ago
3
TrimGalore version 0.6.6 thinks Cutadapt version 2.11 is <1.0

#105 mariadelmarq closed 3 years ago
6
issue for excessive number of cores

#104 dahun73 closed 4 years ago
3
Truseq Methyl capture epic library -specific options for trimming

#103 freedomq8 closed 4 years ago
6
specify output file for pipelines ?

#102 colindaven closed 4 years ago
2
Multicore support issues

#101 dahun73 closed 4 years ago
3
How to enter the Adaptor sequence manually？

#100 Rui-Jing closed 4 years ago
1
python 3.8 incompatibility on Conda?

#99 Blosberg closed 4 years ago
2
Read length vary for sequence in PE fastq files

#98 priyatamapandey closed 4 years ago
10

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