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Old 12-22-2011, 05:19 PM   #1
gene coder
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Location: Ireland

Join Date: Jul 2011
Posts: 18
Default Reverse engineering BAM files: BAM -> FASTQ

How can I possibly extract the reads from a BAM file and put them into a FASTQ file for simulation (maq simutrain, then maq simulate)?

Should I just extract col. 1, 10 and 11 from a BAM file and put them in a text file along with a '+'? That is the output by read simulators.

But does it not happen that DNA sequences and base quality sequences are reversed and/or transformed depending on the direction and strand of reads relative to reference genomes? I would have to fix that too in that case.
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