Illumina single-end data

[MarieLataretu]

I'd add an extra parameter --illumina-single-end (like --nano and --illumina), so that one can clean single- and paired-end reads in one clean run

[hoelzer]

Ah yes, that's a good solution!

MarieLataretu notifications@github.com schrieb am Mi., 20. Mai 2020, 19:55:

I'd add an extra parameter --illumina-single-end (like --nano and --illumina), so that one can clean single- and paired-end reads in one clean run

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[MarieLataretu]

I just scrolled by - Is the renaming of the reads applicable also for the single-end reads?

[hoelzer]

renaming of the reads? do you have an example?

[MarieLataretu]

We do this, before mapping:

  # this is working for ENA reads that have at the end of a read id '/1' or '/2'
  EXAMPLE_ID=\$(zcat ${reads[0]} | head -1)
  if [[ \$EXAMPLE_ID == */1 ]]; then 
    if [[ ${reads[0]} =~ \\.gz\$ ]]; then
      zcat ${reads[0]} | sed 's/ /DECONTAMINATE/g' > ${name}.R1.id.fastq
      TOTALREADS_1=\$(zcat ${reads[0]} | echo \$((`wc -l`/4)))
    else
      sed 's/ /DECONTAMINATE/g' ${reads[0]} > ${name}.R1.id.fastq
      TOTALREADS_1=\$(cat ${reads[0]} | echo \$((`wc -l`/4)))
    fi
    if [[ ${reads[1]} =~ \\.gz\$ ]]; then
      zcat ${reads[1]} | sed 's/ /DECONTAMINATE/g' > ${name}.R2.id.fastq
      TOTALREADS_2=\$(zcat ${reads[1]} | echo \$((`wc -l`/4)))
    else
      sed 's/ /DECONTAMINATE/g' ${reads[1]} > ${name}.R2.id.fastq
      TOTALREADS_2=\$(cat ${reads[1]} | echo \$((`wc -l`/4)))
    fi
  else
[....]```

But I just saw, that we also do this for the ONT data, so I'll implement this also for the Illumina singe-end data!

[hoelzer]

Ah sorry, I got confused with the rnaseq pipeline ;)

Yeah, I introduced this renaming stuff because I experienced problems with some FASTQ headers. I think what we could also have is a more convenient renaming Python script or so that

• renames the reads
• saves the mapping between the original and new ids in a tsv
• restores ids based on the tsv

see: https://github.com/EBI-Metagenomics/emg-viral-pipeline/blob/master/bin/rename_fasta.py

So we could have a separate rename step for any FASTQ, then the filtering happens, and then we have a restore module...

maybe that's cleaner?

But I am also happy with any other simple solution

[MarieLataretu]

yeah, an extra process for renaming would definitely reduce code redundancy!

I'll go for the copy-paste solution for the moment and open a new issue