I have to analyze paired-end RNA-seq read that are in an unusual format: both pair-end reads are joined in one FASTQ. I need to split the file in two separated FASTQ paried-end files.
There are a galaxy tool named FASTQ splitter that can do this:
What it does
Splits a single fastq dataset representing paired-end run into two datasets (one for each end). This tool works only for datasets where both ends have the same length.
Sequence identifiers will have /1 or /2 appended for the split left-hand and right-hand reads, respectively.
A multiple-fastq file, for example:
Do you know any other standard alone script that can do this job?