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Need access to certain fields using BioMap for .bam file reading

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Reut on 16 May 2012
Closed: MATLAB Answer Bot on 20 Aug 2021
When reading a .bam file with bamread function, I can get these fields for each read:
MateReferenceIndex - mate reference sequence
InsertSize - insert size of the pair
both of those fields are part of the sam format. However, when I read the .bam file with BioMap (to save time and memory) - I don't have these fields available.
Is there a way to get these fields using BioMap? (I am using R2012a)
  1 Comment
yishaiy on 18 Apr 2013
Hi Reut, Did you find a way for getting fields from BioMap that are not included in the regular format? Yishai

Answers (2)

Lucio Cetto
Lucio Cetto on 1 Jun 2012
Currently, you'll need to look into the mate, wich you could find using the MatePosition. This is not optimal and would require you to resolve for the right mate, as you know there may be several reads mapped in the sam position as the mate. Lucio
yishaiy on 18 Apr 2013
Hi Lucio, Is there a way of getting fields from BioMap that are not included in the regular format? I want to get the "length" field from a SAM file. using BioMap. Yishai

Vamsee on 26 Nov 2012
Hi Reut and Lucio,
Could you clarify if this was resolved / have you found a workaround?
I'm facing the same issue with BioMap - as it's imperative I can MateReference and InsertSize from within BioMap to be able to find translocations between two chromosomes.
Thank you, Vamsee

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