Question: Maq Output
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gravatar for Michaela Lee
8.8 years ago by
Michaela Lee • 30
Michaela Lee • 30 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 COMMENT • link • modified 8.8 years ago by Anton Nekrutenko ♦ 1.7k • written 8.8 years ago by Michaela Lee • 30
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gravatar for Anton Nekrutenko
8.8 years ago by
Penn State
Anton Nekrutenko ♦ 1.7k 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 http://nekrut.bx.psu.edu http://usegalaxy.org
ADD COMMENT • link written 8.8 years ago by Anton Nekrutenko ♦ 1.7k
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