Can you elaborate? fastq is the input format with sequencing reads,
not the one use generate with Maq. You convert fastq to SAM by
aligning the reads to a reference. So, technically speaking, any
mapper (e.g., BWA, bowtie) is a fastq-to-SAM converter.
On Jan 27, 2010, at 1:11 PM, Michaela Lee wrote:
Does anyone know if Maq can produce alignment data in SAM format?
Currently we can only generate outputs in fastq format. Is there a
way Galaxy can convert a fastq file to a SAM file? I did not see it
as an option but I thought I'd ask. Thanks!
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