Finding the nearest CpG island

Question

[arturo.didonna]

Hi everyone. I hope this is not a FAQ, but I am trying to find out which one is the nearest CpG island relatively to the TSS of several human transcripts of my interest. This is a snip of the info about the transcripts that I already collected:

ID          chrom    strand    txStart     txEnd
uc002bps    chr15    +         91303823    91337600
uc003xba    chr8     +         22022674    22059441
uc002prj    chr19    -         50484910    50523904
uc001dlo    chr1     -         86814420    86862003

Is there any software that would do the job? I looked at home, but I couldn't find examples on how to format the input file.

Thanks in advance.

Arturo

Answer 1

[Chirag Nepal]

Check Bedtools closestBed function