trimmed and val

[DWY1a]

When I used trimgalore, the file sample_1_trimmed.fq.gz was generated, then sample_1_val.fq.gz was generated, and the trimmed file was removed. I generated a full trimmed.fq.gz file during the run, but did not generate a full val.fq.gz, so how do I do this? Can I just start running again?

[FelixKrueger]

Hi there, I am not exactly sure I understand what the problem is but just generally:

• single-end trimming gives rise to files ending in trimmed.fq.gz
• paired-end trimming (--paired) gives rise to the trimmed.fq.gz intermediate files, and validated paired-end trimmed files ending in val_R[12].fq.gz

You can of course re-issue the trimming process from untrimmed fastq.gz files, the newly generated trimmed files and trimming reports will overwrite already existing files.