Hi Folks,
probably a common situation.
Having a Illumina PE dataset (qseq converted to fastq), I'd like to
remove some adapter sequences or clip low quality ends (e.g. with
the fastX toolkit).
Usually I end up having a dataset where there's not always a mate/
counterpart of read1 in read2 fastq, because most tools usually don't
care about pairs. OK.
Are there tools available for e.g. filling dummy sequences in positions
where there is the mate/counterpart missing? Or vice versa, remove
the single read if there is no mate/counterpart?
Or do I have to write it on my own? I am just curious ..
Having a bunch of HiSeq lanes makes this task tedious ;-)
Sven
probably a common situation.
Having a Illumina PE dataset (qseq converted to fastq), I'd like to
remove some adapter sequences or clip low quality ends (e.g. with
the fastX toolkit).
Usually I end up having a dataset where there's not always a mate/
counterpart of read1 in read2 fastq, because most tools usually don't
care about pairs. OK.
Are there tools available for e.g. filling dummy sequences in positions
where there is the mate/counterpart missing? Or vice versa, remove
the single read if there is no mate/counterpart?
Or do I have to write it on my own? I am just curious ..
Having a bunch of HiSeq lanes makes this task tedious ;-)
Sven
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