map bed file to other bed file

Question

[kapil.joshi036]

I have a reference mitocondrial genome bed file

#chr    start   end
TRNF    577 647
RNR1    648 1601
TRNV    1602    1670
RNR2    1671    3229
TRNL1   3230    3304
ND1 3307    4262
 TRNI   4263    4331
 TRNQ   4329    4400
 TRNM   4402    4469
ND2 4470    5511

and i have a bed file of sample

chrM    3192    3966    input.ab1   60  +

now i want to find these co-ordinates belonging gene from the reference bed file

[ivivek_ngs]

If you are aware of bedtools or bedops they will do the trick for you. Try to search for intersection of bed files in biostars and you will find your answers. This is a very simple problem and you should not have much struggle to perform this operation if you read the documents or blog posts concerning this kind of operation. Just remember which file information you need to keep in output file, use the tools accordingly to keep that file as the first input parser for which the output bed file will contain entries matched.

Answer 1

[shaun]

bedtools http://bedtools.readthedocs.io/en/latest/ (intersect bed)