Hi all, My question is to find a method to count enhancer RNAs from RNASeq data. Although it may have been asked before, I could not find any post close to mine. I have a couple of fastq files of RNASeq data. I am using TopHat for alignment. When I put my .bam files to IGV, I can visually see some reads in locations where enhancers bind to. But when it comes to using a tool to count the reads in those locations, although those specific locations are included in my .gtf file with an Ensemble ID, the count is "0".
my code for featureCounts is
../anaconda/bin/featureCounts -a .../bcbio_ku/share/bcbio/genomes/Hsapiens/GRCh37/rnaseq/ref-transcripts.gtf -o .../work/my_generated.counts -t transcript -s 0 -p -C .../final/Unif_DMSO/Unif_DMSO-ready.bam
Is there anyone using an alternative method for enhancer RNA counting? I believe a lincRNA counter or miRNA counter would help me build the method too. The last option for me is to create a unique .gtf file according to "http://enhanceratlas.org/download.php" for each cell line through a python script.