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reading information from a table and apply a command on multiple files

 
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Old 10-02-2012
MySQL reading information from a table and apply a command on multiple files
Hey gyuz,

I wanna calculate the number of mapped reads of a bam file in a region of interest. I used this code to do so :

Code:
samtools view input.bam chrname:region1 > region1.txt

This will store all the reads from given bam file within the region of interest in region1.txt

Now I have several bam files and several regions for each which are different. (regions are not the same in all bam files)

I prepared a list of them like below:

bam1 region1
bam1 region2
bam1 region3
bam2 region4
bam2 region4
bam3 region5

I want the script to read from the table and apply the function on proper bam file and regions and report the output for each region in a single file. region1.txt, region2.txt, region3.txt,.....

If you can help me with this you saved my time so much!!

Thanks in advance.
Last edited by @man; 10-02-2012 at 12:44 PM..
 
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