Hi All,
Is there any way to get all the original B entry(even the ones for which there is no overlap with A as well) in intersectBed utility? I am trying to overlap two bed files. I need all the entry of file B which I put in -b options. I can not switch the file as the size of file A i.e in -a option is very very big.
Thanks
•
written
by
lyfsa •
2 answers
Sort your A and B files first then use the -sorted flag. This will use far less memory, and should allow you to flip the A and B files as you suggest.
Just off the top of my head - you could add one long interval to you file A that covers the entirety of B. Later you can use the name of this artificial interval to distinguish between real and artificial overlaps.
Log in to answer this question.
-
Add all non overlapping genes/transcripts from one gtf to another with bedtools intersect
written by robert.murphy •
-
Determine the significance of peak overlaps (bedtools)
written by kstangline •
-
intersectBed a gtf file with a vcf file
written by Susmita Mandal
-
Understanding IntersectBed columns
written by fadhil.abubaker •
-
How to find overlapping regions among three bed files [Solved]
written by Bioradical •
-
Bedtools Compare Multiple Bed Files to one Bed files?
written by BIOTIN •
-
Getting All Reads That Align To A Region In Compact Bed Format Using Bedtools?
written by user
-
Getting Number Of Reads In Intervals With Bedtools
written by user
-
Intersectbed Tool Generating Empty File
written by bioinfo
-
Bedtools Compare Multiple Bed Files?
written by Bioscientist
