Hi
I extracted reads from a specific region from tophat alignment (bam files) using samtools view. The number of reads I get is 20. When I checked the region using IGV, the only subset of reads actually pass thorough the region. There are few reads that clearly end before the start of the region that I specified. I am very perplexed with this. Someone please enlighten me.
Thanks
I extracted reads from a specific region from tophat alignment (bam files) using samtools view. The number of reads I get is 20. When I checked the region using IGV, the only subset of reads actually pass thorough the region. There are few reads that clearly end before the start of the region that I specified. I am very perplexed with this. Someone please enlighten me.
Thanks
