How to get the total number of reads overlapping RNA regions in R
I have found the overlapping regions of a file of TSS and of RNA. The intersecting reads look like this:
chr1 X108113121 X108113122 chr1.108113121.108113122.. X3 X.
1 chr1 108113470 108113471 chr1:108113470-108113471,- 1 -
2 chr1 237766677 237766678 chr1:237766677-237766678,+ 1 +
3 chr1 91853110 91853111 chr1:91853110-91853111,- 1 -
4 chr1 91853104 91853105 chr1:91853104-91853105,+ 1 +
5 chr10 70770177 70770178 chr10:70770177-70770178,+ 1 +
How can I get the total number of reads overlapping the RNA regions in R? Also, how can I get the percentage of reads contaminated by the RNA?
1 answer
In the GenomicRanges package, there is a findOverlaps() function. You can use that along with a bed file with chr/start/end of all RNA regions you are interested in.
You could also do this outside of R by using the intersect function in bedtools
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