I'm trying to plot "meta" coverage of annotation: i.e. features (eg. gene class) over certain regions. It is similar to read coverage plots over gene body, except my input is two bed files (both in BED6 format) - (A) one containing the regions for which the meta plot is needed, and another being the list of genes or any feature whose coverage over the regions in (A) is needed.
Is there any package or tool which can create such plots (my domain is limited to python but I can try to work with R) ?
Something akin to this but for whole gene body:
- Kelley, D, Rinn, J (2012). Transposable elements reveal a stem cell-specific class of long noncoding RNAs. Genome Biol., 13, 11:R107.
Edit: The BED file containing list of regions looks like this:
chr3 39218734 40053659 region1 0.92426187419769 + chr4 140163762 140453127 region2 0.896103896103896 - chr7 40549151 41205036 region3 0.986072423398329 + chr8 81291743 81963246 region4 0.94184168012924 - chr9 12284032 12539789 region5 0.95539033457249 -
And the bed file containing features to be plotted looks like this:
chr3 39218100 40053200 LINE 1 + chr4 140163962 140453027 LINE 1 - chr7 40549002 41204999 SINE 1 + chr8 81291143 81963846 LTR 1 - chr9 12284332 12539720 LTR 1 -