Filtering Paired End Reads

Question

[brentp]

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.

Answer 1

[Jeremy Leipzig]

You might want to look at this script.

[Jeremy Leipzig]

the next generation, in C

[brentp]

thanks, at least i can use that as a starting point. i'm surprised there isn't a well-known utility for this, it must be common thing to want to do...

[Frédéric Bigey]

Many thanks. It's exactly what I was looking for!

Answer 2

[Louis Letourneau]

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.

Answer 3

[Czh3]

Here is a python script can help you filter low quality paired-end reads. The script deal with the two fq files at the same time, and output file are also paired-ends. (the same reads id and position in two output fastq files.)