I have big wig file of RNA seq and BS seq data.I want to calculate number of overlapping reads of RNA seq that covers the methylated CG.
Which function should I use to count number of overlapps
Hello,
You can use bedtools package. It contains a program intersectBed or intersect it reports all the overlapping co-ordinates of two bed files with -wa and -wb option. Since it is a bigwig file I dont think you have to change to bed format. But read about the format first here http://bedtools.readthedocs.org/en/latest/content/tools/intersect.html.
with a wig and single regions, you can be oldschool and write an AWK one-liner scripy :)
or sort the wig if needed and write a small python (or whatever) script scanning it along
if you have bam and want to be precise - eg HTSEq on the python level
or any counter (featureCount from subread is probably best/fastest now) with a proper/custom GTF/GFF
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