Ecosyste.ms: Issues

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GitHub / FelixKrueger/TrimGalore issues and pull requests

#170 - RRBS data trimming-CGA problem

Issue - State: closed - Opened by MilosCRF about 1 year ago - 5 comments

#169 - Trim-galore not compatible with latest python inside docker container.

Issue - State: closed - Opened by jorgeamaya about 1 year ago - 2 comments

#168 - Trim-galore through Bioconda requires workaround for M1 Macs.

Issue - State: closed - Opened by trev-f about 1 year ago - 1 comment

#167 - merge in changes from master

Pull Request - State: closed - Opened by FelixKrueger over 1 year ago

#166 - Add trimmed sequences to fastq header?

Issue - State: closed - Opened by js72587 over 1 year ago - 8 comments

#165 - Is using an automatically recognized 13bp adapter sufficient?

Issue - State: closed - Opened by user-tq over 1 year ago - 2 comments

#164 - trimming multiple adapters from both reads

Issue - State: closed - Opened by mjbug over 1 year ago - 5 comments

#163 - --paired end specifications

Issue - State: closed - Opened by mjbug over 1 year ago - 2 comments

#162 - valX files vs trimmed files? diff output same code?

Issue - State: open - Opened by desmodus1984 over 1 year ago - 4 comments

#161 - files corrupted after using clock command

Issue - State: closed - Opened by AnastasijaVasilevska over 1 year ago - 3 comments

#160 - trimmed and val

Issue - State: open - Opened by DWY1a over 1 year ago - 1 comment

#159 - Question about default quality filtering

Issue - State: closed - Opened by aepstein96 over 1 year ago - 1 comment

#157 - Trimming .gz files

Issue - State: closed - Opened by samhimes92 over 1 year ago - 5 comments

#156 - Fixed essential bug for decompression default path

Pull Request - State: closed - Opened by FelixKrueger over 1 year ago

#154 - Update master

Pull Request - State: closed - Opened by FelixKrueger over 1 year ago

#153 - update dev

Pull Request - State: closed - Opened by FelixKrueger over 1 year ago

#152 - declaration for "$maxn_fraction"

Pull Request - State: closed - Opened by manogenome over 1 year ago - 2 comments

#151 - get Master up to speed

Pull Request - State: closed - Opened by FelixKrueger over 1 year ago

#150 - Bringing dev up to current state

Pull Request - State: closed - Opened by FelixKrueger over 1 year ago

#149 - Optionally use igzip for decompression of gzipped files.

Pull Request - State: closed - Opened by ghuls over 1 year ago - 1 comment

#148 - Using TrimGalore for different rounds of adaptor cuttings

Issue - State: open - Opened by carmencita almost 2 years ago - 1 comment

#147 - trimgalore and cutadapt in two steps?

Issue - State: open - Opened by marwa38 almost 2 years ago - 6 comments

#146 - Can trimgalore be used to clean up mate pair libraries?

Issue - State: open - Opened by gunjanpandey almost 2 years ago - 3 comments

#145 - Update Ovation RRBS kit info

Pull Request - State: closed - Opened by michael-weinstein almost 2 years ago

#144 - Fixes CPU warning bounds

Pull Request - State: closed - Opened by sclamons almost 2 years ago

#140 - Segmentation fault when disk space is low

Issue - State: closed - Opened by pinin4fjords about 2 years ago - 3 comments

#139 - Run TrimGalore on a FASTA input

Issue - State: closed - Opened by vkkodali about 2 years ago - 1 comment

#138 - equivalent of `--discard-untrimmed` parameter in `trim_galore`

Issue - State: closed - Opened by bounlu about 2 years ago - 1 comment

#137 - `--max_n` value as a fraction

Issue - State: closed - Opened by bounlu about 2 years ago - 4 comments

#136 - After trimming 10 bp at 5', the GC content at 3' changed oddly

Issue - State: closed - Opened by XiaoTW123 about 2 years ago - 3 comments

#135 - TrimGalored sequence cannot be mapped with Bowtie2

Issue - State: closed - Opened by moqri about 2 years ago - 2 comments

#134 - Changelog doesn't mention 0.6.7

Issue - State: closed - Opened by HenrikBengtsson over 2 years ago - 1 comment

#133 - How is an error defined?

Issue - State: closed - Opened by CharlotteAnne over 2 years ago - 2 comments

#132 - Adapter trimming in RRBS

Issue - State: open - Opened by franrodalg over 2 years ago - 13 comments

#131 - Trim-galore fails at quality check for some samples but not others

Issue - State: closed - Opened by bonzay36 over 2 years ago - 3 comments

#130 - adapter+quality trimming followed by hard-trimming

Issue - State: closed - Opened by pmenzel over 2 years ago - 5 comments

#129 - No reads end with "A" after trimming

Issue - State: closed - Opened by hkaspersen over 2 years ago - 2 comments

#128 - cutadapt: error: unrecognized arguments: -f

Issue - State: closed - Opened by samsharr over 2 years ago - 4 comments

#127 - Does TrimGalore handle the Illumina T-overhang

Issue - State: closed - Opened by pcantalupo over 2 years ago - 20 comments

#126 - How to properly specify a basename?

Issue - State: closed - Opened by jolespin almost 3 years ago - 2 comments

#125 - The --nextseq argument doesn't change the parameters of cutadapt

Issue - State: closed - Opened by josephhughes almost 3 years ago - 3 comments

#124 - Cutadapt version error

Issue - State: closed - Opened by Jacob-Ferrier almost 3 years ago - 3 comments

#123 - cutadapt cores option docs are misleading

Issue - State: closed - Opened by keiranmraine about 3 years ago - 1 comment

#122 - FastQC location as argument to trim_galore

Issue - State: closed - Opened by niekwit about 3 years ago - 2 comments

#121 - primerset?

Issue - State: closed - Opened by marwa38 about 3 years ago - 2 comments

#120 - Adapter trimming of Illumina DNA PCR-Free prep sequences

Issue - State: closed - Opened by andrews-matt about 3 years ago - 3 comments

#119 - Incomplete trimming of Illumina adapters

Issue - State: closed - Opened by ag1805x about 3 years ago - 3 comments

#118 - SOLiD sequencing data processing

Issue - State: closed - Opened by dahun73 about 3 years ago - 2 comments

#117 - cutadapt: error: [Errno 2] No such file or directory: 'file.fastq\xa0'

Issue - State: closed - Opened by Hannah1746 over 3 years ago - 2 comments

#116 - Multicore support not enabled

Issue - State: closed - Opened by dahun73 over 3 years ago - 1 comment

#115 - Adapter Content after using TrimGalore

Issue - State: closed - Opened by nicolasalexandre21 over 3 years ago - 3 comments

#114 - Update Trim_Galore_User_Guide.md

Pull Request - State: closed - Opened by eafyounian over 3 years ago - 1 comment

#113 - The report is ok but fastqc result shows trimming process hasn't been done

Issue - State: closed - Opened by xjs1996 over 3 years ago - 4 comments

#112 - FastQC fails after trimming due to "No such file or directory..."

Issue - State: closed - Opened by kubu4 over 3 years ago - 2 comments

#111 - Adapter sequence must contain DNA characters only (A,C,T,G or N)!

Issue - State: closed - Opened by titand98 almost 4 years ago - 2 comments

#110 - Error - adapter trimming

Issue - State: closed - Opened by bioramg almost 4 years ago - 12 comments

#109 - Incompatibility error with latest python 3.9.0

Issue - State: closed - Opened by janstrauss1 almost 4 years ago - 2 comments

#108 - TrimGalore removes overrepresented sequences only from R2, R1 untouched.

Issue - State: closed - Opened by kvn95ss almost 4 years ago - 3 comments

#107 - Question about auto detected adapter sequnces and trimming only 3' or 5' end

Issue - State: closed - Opened by dahun73 almost 4 years ago - 2 comments

#106 - input file

Issue - State: closed - Opened by YspCoder almost 4 years ago - 3 comments

#105 - TrimGalore version 0.6.6 thinks Cutadapt version 2.11 is <1.0

Issue - State: closed - Opened by mariadelmarq almost 4 years ago - 6 comments

#104 - issue for excessive number of cores

Issue - State: closed - Opened by dahun73 about 4 years ago - 3 comments

#103 - Truseq Methyl capture epic library -specific options for trimming

Issue - State: closed - Opened by freedomq8 about 4 years ago - 6 comments

#102 - specify output file for pipelines ?

Issue - State: closed - Opened by colindaven about 4 years ago - 2 comments

#101 - Multicore support issues

Issue - State: closed - Opened by dahun73 about 4 years ago - 3 comments

#100 - How to enter the Adaptor sequence manually？

Issue - State: closed - Opened by Rui-Jing about 4 years ago - 1 comment

#99 - python 3.8 incompatibility on Conda?

Issue - State: closed - Opened by Blosberg about 4 years ago - 2 comments

#98 - Read length vary for sequence in PE fastq files

Issue - State: closed - Opened by priyatamapandey about 4 years ago - 10 comments

#97 - how to set the input files with absolute path

Issue - State: closed - Opened by WellJoea about 4 years ago - 5 comments

#96 - Stdout stderr blocking open3

Issue - State: closed - Opened by aswarren about 4 years ago - 7 comments

#95 - TrimGalore with 10X data

Issue - State: closed - Opened by golharam over 4 years ago - 7 comments

#94 - using --cores

Issue - State: closed - Opened by igordot over 4 years ago - 4 comments

#93 - problem running in paired mode persists

Issue - State: closed - Opened by adamfreedman over 4 years ago - 9 comments

#92 - size of output files

Issue - State: closed - Opened by valentinaOpazo over 4 years ago - 3 comments

#91 - De novo plant genome

Issue - State: closed - Opened by hidvegin over 4 years ago - 6 comments

#90 - Add UMI transfer from R2 to readID for IMPLICON

Issue - State: closed - Opened by FelixKrueger over 4 years ago - 1 comment
Labels: enhancement

#89 - --three_prime_clip_R1 max=99?

Issue - State: closed - Opened by deanpettinga over 4 years ago - 2 comments

#88 - Trim Galore vs Cutadapt Handling of Paired-End Reads

Issue - State: closed - Opened by pdellorusso over 4 years ago - 3 comments

#87 - fastqc after trimming

Issue - State: closed - Opened by yeroslaviz over 4 years ago - 1 comment

#86 - Using a fasta file with multiple adapter sequences for trimming

Issue - State: closed - Opened by tobjores over 4 years ago - 11 comments

#85 - Error related to cutadapt version 2.5

Issue - State: closed - Opened by xie186 over 4 years ago - 3 comments

#84 - Error during unning trim_galore

Issue - State: closed - Opened by krunal2406 over 4 years ago - 2 comments

#83 - fix incorrect argument abbreviation

Pull Request - State: closed - Opened by DaGaMs over 4 years ago

#82 - Why the “—paired” process reads in “single-end” mode?

Issue - State: closed - Opened by HeXY0515 over 4 years ago - 1 comment

#81 - failed per base sequence content & kmer content.

Issue - State: closed - Opened by sjfleck over 4 years ago - 2 comments

#80 - v0.6.5 release tar ball contains v 0.6.4 dev

Issue - State: closed - Opened by jjv5 over 4 years ago - 1 comment

#79 - Steps in Trim galore

Issue - State: closed - Opened by Hedi65 over 4 years ago - 4 comments

#78 - TrimGalore only detects python 2, but I have python 3

Issue - State: closed - Opened by ejwright39 over 4 years ago - 5 comments

#77 - more details about -e : Maximum allowed error rate

Issue - State: closed - Opened by Shicheng-Guo over 4 years ago - 9 comments

#76 - How to add custom adaptors in Trim Galore?

Issue - State: closed - Opened by Shicheng-Guo over 4 years ago - 2 comments

#75 - Paired end trimming WGBS

Issue - State: closed - Opened by demis001 over 4 years ago - 13 comments

#74 - polyA option

Issue - State: closed - Opened by xiaoyunguo over 4 years ago - 3 comments

#68 - Trim Galore exit signal: '512'

Issue - State: closed - Opened by hailee-s almost 5 years ago - 2 comments

#65 - Error while running Trim_galore

Issue - State: closed - Opened by Huang-XN about 5 years ago - 13 comments

#63 - Per Base Sequence Content after Adapter Removal

Issue - State: closed - Opened by cazzlewazzle89 about 5 years ago - 6 comments