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Need access to certain fields using BioMap for .bam file reading
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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)
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yishaiy
il 18 Apr 2013
Hi Reut, Did you find a way for getting fields from BioMap that are not included in the regular format? Yishai
Risposte (2)
Lucio Cetto
il 1 Giu 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
Vamsee
il 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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