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Old 01-03-2012, 04:31 AM   #4
david.tamborero
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Location: spain

Join Date: Feb 2011
Posts: 60
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Just in case anyone is interested in this post, I should say that everything goes nice when the two files containing each paired end are merged by the ill2fastq.pl script and then inputted to the bfast commands.

I'm still concerned in the following though:

- which is the advantage of doing so as compared to align each paired end separately and then joining the two resulting sam files (by samtools merge, for instance).

- since i've noticed that the ill2fastq.pl script reverses and complements the second paired end, I'm not sure of what are the correct values for the -w argument in the bfast match ('to find matches on the designed strands') and the -R in the bfast postprocess ('specifies to expect paired reads to be on reverse strands').

cheers,
david
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