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For the 5500's paired-end 75bp/35bp bp files [F3.csfasta, F3.QV.qual] and [F5.csfasta, F5.QV.qual], am I doing this right?
1. I first use solid2fastq to convert the first pair to F3.fastq and the second pair to F5.fastq.
2. Then, with a simple perl script, I merge those two files into a single F.fastq file alternating the 4-line record sets from the F3 and F5 fastq files, the 4 front-read F3 records preceding the 4 end-read F5 records, and so on.
3. I then use the single merged colorspace F.fastq file as input into bfast match.
I just want to be sure I don't have to worry about some kind of "reverse complementing" (or something) for those F5 reads.
-- Fred P.
1. I first use solid2fastq to convert the first pair to F3.fastq and the second pair to F5.fastq.
2. Then, with a simple perl script, I merge those two files into a single F.fastq file alternating the 4-line record sets from the F3 and F5 fastq files, the 4 front-read F3 records preceding the 4 end-read F5 records, and so on.
3. I then use the single merged colorspace F.fastq file as input into bfast match.
I just want to be sure I don't have to worry about some kind of "reverse complementing" (or something) for those F5 reads.
-- Fred P.