How to obtain InsertSize from a BioMap object?
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Is there a way of obtaining the InsertSize field (available using bamread) when opening a bam file as a BioMap object? Opening the bam files using a BioMap object is much faster compared to the bamread function, but I can't find any way of obtaining the InsertSize (TLEN from the corresponding sam file)...
Luuk van Oosten 2015년 1월 26일
If you use something like:
BAMStruct = bamread(File,RefSeq,Range)
You get a struct. from this you can obtain the InsertSize by using something like:
x = BAMStruct.InsertSize
In the examples of the help doc (which are here) you will find something similar; they show an example how they extract instead of the 'InsertSize' the 'Position' by using the following:
data_one = bamread('ex1.bam','seq1', [100 300]);