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Old 12-20-2011, 10:12 AM   #1
Location: spain

Join Date: Feb 2011
Posts: 60
Default how to merge paired ends provided in separate files during (bfast) alignement


I want to align illumina paired-end reads by using bfast. The point is that each end is provided in two separate .fastq files. I am not sure (at all) of which is the best way to 'join' them during the alignement process. I am using bfast_match + bfast_localign + bfast_postprocess. I've seen in the bfast manual that the localalign step allows to do the following:

bfast localalign -1 file_1.bmf -2 file_2.bmf -A 0 -U > sample.baf
When the .bmf file comes from the bwaaln utility. However, when the .bmf file comes from the bfast_match, the following does not seem to work (bfast+bwa-0.6.4e):

bfast localalign -f hg19.fa -m pair_1.bmf -m pair_2.bmf -A 0 -U > sample.baf
Therefore, I do not know the best way to proceed. My lucky guess is to align each .fastq file separately, and when I get the resulting two .sam files for each end then to join them by using picard (or samtools) merge.

Any help will be appreciated!

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