Hi,
I am trying to find the number of mapped reads in a given window. And to be more precise i want to find number of mapped reads for a series of windows. I divided the genome into 100bp and would like to know what are the number of mapped reads in these window. The final aim would be to put these into plink format (as phenotypes).
Is there any tool to do this?
thanks
Hi Thanks. I was trying the bam2bed feature yesterday and it took a lot of time to convert. Is this expected? I couldn't try out the counting the reads bit yet. The --count command, does it count the mapped reads or all reads? thanks
Yes, the conversion can take a lot of time (enough time to read the file and write another one, at least). The count command counts reads overlapping with the windows.bed windows; unmapped reads do not overlap any windows, so they are not counted.