I have paired end read data in R1 and R2 I mapped by using Bowtei2. R1.sam
and R2.sam.
I have converted sam file to bam file and sorted and index it by using
*samtools view -bS R1.sam | samtools sort - R1_sorted*
*samtools index R1_sorted.bam *
now I want to extract all the reads that map on chr1:x-y position,
chr2:x'-y',chr1:x''-y'' ete etc.
i have total 8000 coordinates through out genome. I want to extract all the
reads that mapped at all the 8000 coordinates.
letter find out same for the R2_sorted.bam.
in next step I have to find out how many reads are common (in terms of
similar ids with indication of r1 and R2 reads) between two different
coordinates.
thank you four your kind help
--
*------------------------------------------------------------------------------------------------------*
*Raghvendra Singh*
* Center of Bioinformatics*
* Nehru Science Center.*
* IIDS.*
* University of Allahabad. +91-9559019566*
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