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

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)

[yishaiy]

Hi Reut, Did you find a way for getting fields from BioMap that are not included in the regular format? Yishai

Answer 1

[Lucio Cetto]

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

[Reut]

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]

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

Answer 2

[Vamsee]

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