merging coverage and gene annotation

Question

[schelarina]

Hello,

I have an RNAseq coverage per position file created with bedtools. I would like to include in this file an additional column containing the genome annotation from gff file..Something like this

Chr     Position   Coverage    Annotation
Chr1    1          25          gene X
Chr1    2          27          gene X
Chr1    3          39          gene X
..

Thanks!

[Ashutosh Pandey]

You can use "bedtools intersect" and intersect your bed file with your gff file

http://bedtools.readthedocs.org/en/latest/content/tools/intersect.html