Generally, I use fastx-toolkit to filter fastq-formatted reads, but I'd like something that will filter both ends from a pair of fastq files (creating a new, filtered pair) if either end doesn't meet a given criteria.
Does this exist in a well-known toolkit somewhere? I'd like to be able to trim low quality ends independently. Yes, this is simple to implement, but I'd rather use an existing solution if it's available.
3 answers
You might want to look at this script.
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written
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Jeremy Leipzig
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written
by
Jeremy Leipzig
Many thanks. It's exactly what I was looking for!
You could just use fastx on both file independently. A problem arises only if one of the 2 is completely eliminated because of too strict settings.
Although I agree that Jeremy Leipzig's method avoids this problem since there is a 'SINGLE' output.
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