Originally posted in the old forum by mark on 26.03.2013 - 16:56
I have Illumina reads in _1.fastq and _2.fastq format, but they don't have /1 and /2 in the identifiers. And, note that I only have 1 row with identifiers (starting with @, those starting with + are removed, probably because its redundant).
by katharina on 27.03.2013 - 12:25
I suggest you simply chop off everything in the read headers (the 1st, 5th, 9th, ... row that begins with an @) that occurs after the first space, and add a pairedness indicating ending.
Before deciding on a suitable ending for entire file, I suggest you build yourself a toy dataset to check in the output of tophat whether the pair-indicating ending gets cleaved off in the current version, or not. If it gets cleaved off, choose a different pair-indicating string that does not get deleted in the output, and later replace it in the output by one of the endings that is accepted by our tools (/1,/2 or -1,-2).
Katharina