I want to count the number for each feature: enhancer, promoter, exon, intron and so on for my bed file. Is there any prepared bed tables which can be used to make the intersect and do the counts statistic.
1, Perl or R script and implemented file of Java or python would be appreciated.
2, Is there more professional pipelines to classify batch of genome intervals into different categories? such as enhancer, promoter, exon, intron, miRNA, lncRNA, intergenic and so on?
3, now we can kg2bed, gff2bed, is there any tool called refgene2bed?
The caterogies of the features in Pierre Lindenbaum is too limited. More features such as downstream, intergenic are needed.
Martombo mentioned we can use bed2bam to transfer bed to bam and then use read_distribution.py in RSeQC to do this job