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.