Comments (2)
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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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
—
Reply to this email directly or view it on GitHub.—
Reply to this email directly or view it on GitHub
#13 (comment)
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Related Issues (10)
- add datamash examples
- bug in sed 's/[ \t]*$//' example
- add sed to count the occurrences of each symbol in a fasta file HOT 3
- Awk search command is not working HOT 1
- Command for listing everything that does not match a patter requires extended globing be enabled
- H
- Faster option for "Untangle a FASTQ file. If a FASTQ file has paired-end reads intermingled" HOT 3
- Add aliases from alias.sh
- PDF creation script HOT 3
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