Question: Maq Output
gravatar for Michaela Lee
8.8 years ago by
Michaela Lee30
Michaela Lee30 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! Michaela
galaxy • 928 views
ADD COMMENTlink modified 8.8 years ago by Anton Nekrutenko1.7k • written 8.8 years ago by Michaela Lee30
gravatar for Anton Nekrutenko
8.8 years ago by
Penn State
Anton Nekrutenko1.7k wrote:
Michaela: 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. a. Anton Nekrutenko
ADD COMMENTlink written 8.8 years ago by Anton Nekrutenko1.7k
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