Does anyone know if Maq can produce alignment data in SAM format?
we can only generate outputs in fastq format. Is there a way Galaxy
convert a fastq file to a SAM file? I did not see it as an option but
thought I'd ask. Thanks!
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.