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

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Reut
Reut 2012-5-16
关闭： MATLAB Answer Bot 2021-8-20
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 个评论
yishaiy
yishaiy 2013-4-18
Hi Reut, Did you find a way for getting fields from BioMap that are not included in the regular format? Yishai

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回答（2 个）

Lucio Cetto
Lucio Cetto 2012-6-1
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
  2 个评论
Reut
Reut 2012-6-3
Hi Lucio,
thank you for the answer, but I am not sure I understand -
How can I look into the mate, if I don't know on which reference sequence (chromosome) it is?
and how do I get the insertSize?
thanks
Reut
yishaiy
yishaiy 2013-4-18
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
Vamsee 2012-11-26
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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