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Old 05-18-2015, 05:54 PM   #1
hujiacun
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Default how to find out mate reads?

Hi,
When I got the BAM file of alignments in the region of interest, how to retrieve the mate's data? I want to know how those mates are distributed throught the whole genome.
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Old 05-19-2015, 04:47 PM   #2
student-t
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Can you just visualize them on a viewer such as IGV?
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Old 05-19-2015, 05:06 PM   #3
hujiacun
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Quote:
Originally Posted by student-t View Post
Can you just visualize them on a viewer such as IGV?
student-t, thanks for your reply.
I use "samtools view originalfile.bam Chr4:100k-200k" to get a regional BAM file. In IGV, I can visualize the reads among my interested region. Because of Structure Viaration, the mates of those reads may not locate in the same region, and are not included in the BAM file.
How can I get a file including data of those mates?
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Old 05-29-2015, 05:48 AM   #4
maubp
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Do you want to do this by hand/eye in a viewer? If so look at the full BAM file and the viewer should be able to show you the partner read (try right clicking etc). This is possible with Tablet via the tool tip, and you can right click to jump to the partner etc:
https://ics.hutton.ac.uk/tablet/

Or, you can do this programatically by parsing the SAM/BAM file (e.g. in Python using pysam). There are specific columns used to report the mapping position of the partner read.
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