Run BBC and DH through tophat pipeline
Running through iPlant
Tophat complete
All data @
_ next need to
Use the coverageBed command from BEDTools[QH10] (or another equivalent method) to count the number of reads that align to all exons in annotated union transcripts (see listing 1).
robertsmac:bin sr320$ ./coverageBed -split -abam /Volumes/web/cnidarian/AltSplice_Tophat_BB3_DH/solid0078_20091105_BB3_out/accepted_hits.bam -b /Volumes/Bay3\ scratch/dwnload/oyster.v9.glean.final.rename.gff > /Users/sr320/Desktop/covBed_countedHits_BB3.gff
