Filtering Paired End Reads
3
8
Entering edit mode
12.4 years ago
brentp 24k

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.

fastq fastx filter • 13k views
ADD COMMENT
9
Entering edit mode
12.4 years ago

You might want to look at this script.

ADD COMMENT
5
Entering edit mode
ADD REPLY
0
Entering edit mode

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...

ADD REPLY
0
Entering edit mode

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

ADD REPLY
2
Entering edit mode
12.4 years ago

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.

ADD COMMENT
0
Entering edit mode
7.7 years ago
Czh3 ▴ 190

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.)

ADD COMMENT

Login before adding your answer.

Traffic: 1867 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6