bam to fastq one liner

[LukeBraidwood]

Hey,

Thanks very much for putting these explanations and tools up. I think the one liner you have put for converting bam to fastq is inappropriate (or should be described differently). The problem is that your awk prints fields 1, 10, and 11 in the bam.

Field 10 is called SEQ and represents the query sequence to which the read is aligned. However alignment sequences are always represented on the plus strand of the reference (http://chagall.med.cornell.edu/NGScourse/SAM.pdf, http://genome.sph.umich.edu/wiki/SAM), meaning that for stranded bams this tool is inappropriate.

Thanks,

Luke

[stephenturner]

Thanks. Suggestion / pull request welcomed.

Stephen

Sent from mobile.

On Jun 15, 2015, at 10:26 AM, LukeBraidwood [email protected] wrote:

Hey,

Thanks very much for putting these explanations and tools up. I think the one liner you have put for converting bam to fastq is inappropriate (or should be described differently). The problem is that your awk prints fields 1, 10, and 11 in the bam.

Field 10 is called SEQ and represents the query sequence to which the read is aligned. However alignment sequences are always represented on the plus strand of the reference (http://chagall.med.cornell.edu/NGScourse/SAM.pdf, http://genome.sph.umich.edu/wiki/SAM), meaning that for stranded bams this tool is inappropriate.

Thanks,

Luke

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[LukeBraidwood]

Dear Stephen,

Sorry for the slow reply, just remembered this exchange. I'm currently
using the samtofastq tool from picard tools, which has an option to
regenerate the RC of alignments to the negative strand:
http://broadinstitute.github.io/picard/command-line-overview.html#SamToFastq

Cheers,

Luke

On Mon, Jun 15, 2015 at 4:36 PM, Stephen Turner [email protected]
wrote:

Thanks. Suggestion / pull request welcomed.

Stephen

Sent from mobile.

On Jun 15, 2015, at 10:26 AM, LukeBraidwood [email protected]
wrote:

Hey,

Thanks very much for putting these explanations and tools up. I think
the one liner you have put for converting bam to fastq is inappropriate (or
should be described differently). The problem is that your awk prints
fields 1, 10, and 11 in the bam.

Field 10 is called SEQ and represents the query sequence to which the
read is aligned. However alignment sequences are always represented on the
plus strand of the reference (
http://chagall.med.cornell.edu/NGScourse/SAM.pdf,
http://genome.sph.umich.edu/wiki/SAM), meaning that for stranded bams
this tool is inappropriate.

Thanks,

Luke

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