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gene coder 12-22-2011 05:19 PM

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.

raonyguimaraes 12-22-2011 05:57 PM


Richard Finney 12-22-2011 06:39 PM

Check out for bampe2fq.c and bamse2fq.c for fast implementations of bam to fastq programs. It handles your concerns about reverse complimenting the sequence and reversing the quality string.

gene coder 01-03-2012 03:42 PM

Thanks. I found that SamToFastq in Picard did the job on a chromosome of NA12878 from the 1000 Genomes Project.

1. I separated SE reads and PE reads by library into separate BAM files using SamTools.
2. For PE reads, I also had to get rid of read-pairs that were unmapped (bit 3) or whose mate was unmapped (bit 4) or that were not properly aligned (bit 2).
3. I further separated the BAM files by read length.
4. Each BAM file now contained SE or PE reads only of the same read length and the same library.
5. Now I could run SamToFastq to convert a SAM file to a DAT file for use with MAQ simutrain.

Those were the steps to do to get what I wanted.

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