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Allow adding of Illumina Casava 1.8 format entry to fastq headers #41
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Hi Charles, Thanks, |
Great, thanks. I'll follow along :) In the meantime I've just got the following hacky code in my Nextflow script which does the job:
|
I'll add this in the next release, hopefully this week |
Released in 2.0.0 |
Hi,
Thanks for the useful tool. Would it be possible to add the option to modify the headers of the output fastq files? I can see in
aligner.py
that the (final) command for generating clean reads with paired-end data is:This results in read headers in the form of "@<read_id>/1". It would be useful to have the option to output clean reads with the Illumina Casava 1.8 format entry, which is an option in
samtools fastq
:Minimally, the command could be:
This results in read headers in the form of "@<read_id> 1:N:0:0".
In my case this is useful because my previous method of host decontamination (
bowtie2 ... --un-conc-gz id.unmapped.fastq.gz ...
) resulted in read headers in that format, and hence downstream read manipulation is based on that format. However, I can understand if this might not be a priority to implement. If not, could there be an option to save a *.bam file with clean reads, allowing users to also extract reads to file as they see fit?Thanks
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