Finding intergenic transcripts from a bedgraph file or bam file
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8.7 years ago
harris • 0

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

RNA-Seq • 2.4k views
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Entering edit mode
8.7 years ago

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

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