I have a bunch of Illumina PE data that has been run through fastx trimmer and clipper. I am ready to map these reads, but am needing to create 2 files for paired end reads (the left and right hand reads in separate files) and a file with the orphaned reads. Of course the paired end files need to have the reads in the same order.
This has to be a common problem, but I can't seem to find a tool that parses fastq files in this way (I swear I searched the Biostar forum).
Any help would be greatly appreciated.
NP