How to obtain InsertSize from a BioMap object?

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Razvan 2015-1-26

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https://ww2.mathworks.cn/matlabcentral/answers/171761-how-to-obtain-insertsize-from-a-biomap-object

编辑： Razvan 2015-2-7

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)...

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Answer 1

Luuk van Oosten 2015-1-26

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https://ww2.mathworks.cn/matlabcentral/answers/171761-how-to-obtain-insertsize-from-a-biomap-object#answer_165942

在 MATLAB Online 中打开

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]);
data_one(27).Position

Good luck!

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Luuk van Oosten 2015-1-28

Can you provide a .bam file for me and you code? I'll give it a try!

Razvan 2015-1-31

编辑：Razvan 2015-2-7

Thanks for spending your time on this! Here is a BAM file and some Matlab code that illustrates my problem: https://app.box.com/s/e3sjphe802z616gzwzelse0o89py6vlm

If you run my script from that folder, you'll see the 2 ways that I know to open a bam file and to compute the fragment lengths. Using bamread, the TLEN field from the SAM/BAM file is easily accessible. Using BioMap objects, the TLEN/InsertSize information is not available anymore and one needs to match the headers of the reads in order to compute to total fragment length. The problem is that bamread is very slow in comparison with BioMap (3s vs. 0.2s), and sorting the headers of millions of reads is also pretty slow. It would be much better if BioMap would simply load the TLEN field of the SAM/BAM files. This is available information stored in the SAM/BAM file which is simply disregarded by BioMap (as far as I know). Any chance of getting this TLEN info using the faster BioMap loading function?

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