After a quick search I found these:
Hydra
Picard (SAMToFastq)
HudsonAlpha
Possibly EMBOSS
Any comments on these? Any other options for BAM-to-FASTQ conversion?
Basically I want to recover all paired-end reads (both R1 and R2) that were fed into the alignment that produced the BAM file, whether they mapped successfully or not.
Hydra
Picard (SAMToFastq)
HudsonAlpha
Possibly EMBOSS
Any comments on these? Any other options for BAM-to-FASTQ conversion?
Basically I want to recover all paired-end reads (both R1 and R2) that were fed into the alignment that produced the BAM file, whether they mapped successfully or not.
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