Hi Raghvendra, Make a BED file with the regions of interest, one per line and then:
samtools view -L roi.bed alignments.sorted.bam > subset.alignments.sorted.bam Best, Devon ____________________________________________ Devon Ryan, Ph.D. Email: [email protected] Tel: +49 (0)178 298-6067 Molecular and Cellular Cognition Lab German Centre for Neurodegenerative Diseases (DZNE) Ludwig-Erhard-Allee 2 53175 Bonn, Germany On May 28, 2014, at 8:47 PM, raghvendra singh wrote: > 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 > ------------------------------------------------------------------------------ > Time is money. Stop wasting it! Get your web API in 5 minutes. > www.restlet.com/download > http://p.sf.net/sfu/restlet_______________________________________________ > Samtools-help mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/samtools-help ------------------------------------------------------------------------------ Time is money. Stop wasting it! Get your web API in 5 minutes. www.restlet.com/download http://p.sf.net/sfu/restlet _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
