Finding intergenic transcripts from a bedgraph file or bam file

Question

[harris]

Hi, I have a series of bedgraph files made from bam files using

bedtools-2.17.0/genomeCoverageBed -ibam my.sorted.bam -bg > my.sorted.bg 

command. I can load into UCSC browser and works fine. Now my question is, I did paired end strand specific libraries and analysis. From my .bg files I want to find the intergenic transcripts Ie ncRNAs, possible eRNAs( a complete list with positions that I can then work with). I have another file with the chromsome and start and stop of all the transcriptions units, about 23,000 (from a cufflink file). How do I use bedtools or any tool to find the transcripts that are NOT in the transcription units? Thanks for any help. I know this is basic, but I have to start somewhere. Thanks for any help.

Steve

Answer 1

[Sukhi Singh]

For the second question, use intersectBed with -v parameter on the bedGraph file and file transcript location.

-v Only report those entries in A that have no overlap in B. Restricted by -f and -r.

From my .bg files I want to find the intergenic transcripts Ie ncRNAs, possibe eRNAs( a complete list with positions that I can then work with)

You have to fetch files for the locations you want to work with (intergenic, exon, intron etc) and again use intersectBed

[harris]

Thanks so much Sukhdeep, will give your thoughts a try. steve