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Illumina single-end data #4
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I'd add an extra parameter |
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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I just scrolled by - Is the renaming of the reads applicable also for the single-end reads? |
renaming of the reads? do you have an example? |
We do this, before mapping:
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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
see: So we could have a separate maybe that's cleaner? But I am also happy with any other simple solution |
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 |
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