FelixKrueger/TrimGalore

Issues

• Parallel processing of paired-end fastq files

  #195 opened 2 months ago by PramodRaoB
  2

• support BGISEQ/DNBSEQ/MGISEQ?

  #196 opened 2 months ago by orangeSi
  9

• 1-8 % of PolyA always remains in the R1 of my RRBS trimed PE files

  #194 opened 5 months ago by Muhyees
  2

• Trim just one read in paired-end data by TrimGalore

  #193 opened 6 months ago by iranianuser
  4

• question about trimming

  #192 opened 6 months ago by hidvegin
  4

• Queries regarding TrimGalore

  #191 opened 6 months ago by unikill066
  3

• trimming multiple adapters from both reads

  #164 opened 2 years ago by mjbug
  9

• Trim Galore frozen at adapter trimming step

  #190 opened 8 months ago by faye-romero
  3

• Does TrimGalore do soft clipping by default?

  #189 opened 8 months ago by tarunaaggarwal
  6

• ask for help in removing the first 10 nt random barcode in the 5’ end

  #188 opened 9 months ago by Shuixin-Li
  1

• Trim_galore directional vs. non-directional mode

  #177 opened a year ago by shaghayeghsoudi
  4

• Trimgalore seems to detect only a very low % of reads in the files that had adapters to trim (<40% of the reads)

  #187 opened 10 months ago by dthirupp
  4

• Adapter Trimming on PE reads have different number of reads output

  #186 opened 10 months ago by bshim181
  1

• Trim galore config for pacbio data

  #185 opened 10 months ago by YutongLei2020
  2

• Add new option `--cutadapt_args` to pass on additional params

  #184 opened 10 months ago by FelixKrueger
  0

• trimmed and val

  #160 opened 10 months ago by DWY1a
  1

• Change processing strategy for `--clock` option

  #183 opened a year ago by FelixKrueger
  1

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

  #143 opened a year ago by bmillerlab
  3

• Using TrimGalore for different rounds of adaptor cuttings

  #148 opened 2 years ago by carmencita
  4

• md5sum

  #182 opened a year ago by zhangqc723
  1

• TrimGalore calls pigz when not required

  #181 opened a year ago by kaushikr3
  2

• High PolyA content in R2 reads after trimming.

  #180 opened a year ago by AmrSaadeldin
  3

• problems installing via conda/mamba

  #179 opened a year ago by mawa86
  1

• Trim galore gets stuck on quality and adapter trimming

  #178 opened a year ago by aman-akash
  3

• Please provide an even number of input files for paired-end FastQ trimming! Aborting ..

  #176 opened a year ago by shaghayeghsoudi
  2

• Trimming for xGen™ Methyl-Seq DNA Library Prep Kit

  #174 opened a year ago by abearab
  4

• TrimGalore Citation

  #175 opened a year ago by Leo-ccc
  1

• Validation fails when FASTA files used as input

  #173 opened a year ago by vkkodali
  4

• Conda installation of trim_galore uses really old version of cutadapt

  #172 opened a year ago by vkkodali
  2

• TrimGalore

  #171 opened a year ago by eneubauer29
  1

• RRBS data trimming-CGA problem

  #170 opened a year ago by MilosCRF
  5

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

  #169 opened a year ago by jorgeamaya
  2

• Is using an automatically recognized 13bp adapter sufficient?

  #165 opened a year ago by user-tq
  2

• Trim-galore through Bioconda requires workaround for M1 Macs.

  #168 opened a year ago by trev-f
  1

• Add trimmed sequences to fastq header?

  #166 opened a year ago by js72587
  8

• valX files vs trimmed files? diff output same code?

  #162 opened 2 years ago by desmodus1984
  4

• files corrupted after using clock command

  #161 opened 2 years ago by AnastasijaVasilevska
  3

• --paired end specifications

  #163 opened 2 years ago by mjbug
  2

• Question about default quality filtering

  #159 opened 2 years ago by aepstein96
  1

• UnicodeEncodeError: 'ascii' codec can't encode character '\xb5' in position 2492: ordinal not in range(128)

  #158 opened 2 years ago by anoopsanal
  3

• Trimming .gz files

  #157 opened 2 years ago by samhimes92
  5

• Use of uninitialized value $decompression_path in concatenation (.) or string at /home/sli1/miniconda3/envs/atac3/bin/trim_galore line 2671.

  #155 opened 2 years ago by shl129
  4

• trimgalore and cutadapt in two steps?

  #147 opened 2 years ago by marwa38
  6

• Can trimgalore be used to clean up mate pair libraries?

  #146 opened 2 years ago by gunjanpandey
  3

• cutadapt: error: unrecognized arguments: -f P2_A01_M_0001.fastq Cutadapt terminated with exit signal: '512'.

  #141 opened 2 years ago by sevmurdock
  4

• Can anyone explain Why in default mode -- paired --retain_unpaired only read2 read are retain and not read1

  #142 opened 2 years ago by veeramv
  5

• Segmentation fault when disk space is low

  #140 opened 2 years ago by pinin4fjords
  3

• Run TrimGalore on a FASTA input

  #139 opened 2 years ago by vkkodali
  1

• equivalent of `--discard-untrimmed` parameter in `trim_galore`

  #138 opened 2 years ago by bounlu
  1

• `--max_n` value as a fraction

  #137 opened 2 years ago by bounlu
  4