How to "chop" a large FASTQ PE file in half?

cement_head · 08-07-2017, 06:26 AM

Hello,

I hesitate to use the following terms: "split", "partition", "trim" - because they all have special connotations.

What I'd like to do is to take a large FASTQ file of PE reads and cut the file into two approximately equal halves. However, I want to do it in such a manner that a given file does not have only one half of a pair of a PE read group. In other words, I want to insure that when the file is halved, or split, that no PE reads are separated.

For example, if I have a file with 11 PE reads, I do NOT want 5 reads in one file and 6 reads in another.

Will FASTQ Splitter work for what I want?

- Andor

GenoMax · 08-07-2017, 06:49 AM

Quote:

Originally Posted by cement_head

Hello,

For example, if I have a file with 11 PE reads, I do NOT want 5 reads in one file and 6 reads in another.

- Andor

How would you split a PE dataset otherwise? I assume your PE reads are in two separate files (R1/R2) and the split would have to split both files?

cement_head · 08-07-2017, 08:29 AM

Quote:

Originally Posted by GenoMax

How would you split a PE dataset otherwise? I assume your PE reads are in two separate files (R1/R2) and the split would have to split both files?

No, there are in ONE file, PE reads, RAW FASTQ.

GenoMax · 08-07-2017, 09:11 AM

So your paired-end reads are interleaved? Why not use "split -n 2" to divide the original into to two parts. If you have an odd number of fastq records then using an explicit "split -l ((n+1)/2*4)" may be better (n = number of fastq records).

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08-07-2017, 06:26 AM	#1
cement_head Senior Member Location: Oxford, Ohio Join Date: Mar 2012 Posts: 253	How to "chop" a large FASTQ PE file in half? Hello, I hesitate to use the following terms: "split", "partition", "trim" - because they all have special connotations. What I'd like to do is to take a large FASTQ file of PE reads and cut the file into two approximately equal halves. However, I want to do it in such a manner that a given file does not have only one half of a pair of a PE read group. In other words, I want to insure that when the file is halved, or split, that no PE reads are separated. For example, if I have a file with 11 PE reads, I do NOT want 5 reads in one file and 6 reads in another. Will FASTQ Splitter work for what I want? - Andor

08-07-2017, 09:11 AM	#4
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,080	So your paired-end reads are interleaved? Why not use "split -n 2" to divide the original into to two parts. If you have an odd number of fastq records then using an explicit "split -l ((n+1)/24)" may be better (n = number of fastq records). Last edited by GenoMax; 08-07-2017 at 09:28 AM.*