Bowtie / Feature Requests / #58 Bowtie Number of Perfect Hits

Bowtie Number of Perfect Hits

#58 Bowtie Number of Perfect Hits

Status: open

Owner: Ben Langmead

Labels: bowtie (72)

Priority: 4

Updated: 2011-04-04

Created: 2011-04-04

Creator: Anonymous

Private: No

Hello,

I am using Bowtie to align reads to assembled contigs, requiring perfect match and outputting all hits for each read. Among other things, I am interested in knowing the number of perfect hits for each read. In the SAM format specification, it mentions an optional tag "H0:i:<number_of_perfect_hits>". However, I can find no mention of this tag in the Bowtie SAM output description:
http://bowtie-bio.sourceforge.net/manual.shtml#sam-bowtie-output

Is there any way to get Bowtie to use this tag, or some other way to get this information without scanning through the entire output file to count the alignment lines for each read?

~Thanks,
Lucas Swanson

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Anonymous - 2011-04-04

priority: 5 --> 4

- **priority**: 5 --> 4

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#58 Bowtie Number of Perfect Hits

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