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Maq output

eprimer3 missing?

pysam egg

Michaela Lee

Wednesday, 27 January 2010 Wed, 27 Jan '10

6:11 p.m.

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

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Anton Nekrutenko

Thursday, 28 January Thu, 28 Jan

9:54 p.m.

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. 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! Michaela _______________________________________________ galaxy-user mailing list galaxy-user(a)lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user

Anton Nekrutenko http://nekrut.bx.psu.edu http://usegalaxy.org

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Anton Nekrutenko
Michaela Lee