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Old 12-16-2009, 02:38 AM   #1
lindseyjane
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Location: Oxford

Join Date: Apr 2009
Posts: 28
Default BFAST input format for paired end reads

I would like to know what I should do to input paired end reads to the BFAST software. The script provided, qseq2fastq.pl requires qseq files but I only have the sequence files from the Illumina machine named
e.g.
s_1_1_sequence.txt containing reads from 1st read in lane 1
s_1_2_sequence.txt containing reads from 2nd read in lane 1

I can easily convert to fastq using maq sol2sanger, but I understand that the BFAST FASTQ format is different from the standard FASTQ. The manual states it requires the pairs to be listed in order of 5' to 3' and on the same strand. It also requires them to have the same name whereas at the moment they have the same names but slightly different suffixes of #0/1 for read 1 and #0/2 for read 2.

Does anyone know a quick way to get my reads into the right format? Thanks
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