Hi Galaxy Community Galaxy, we mapped sequence reads from our RNA-Seq experiment to the S. Pome genome (see for your reference Galaxy | Accessible History | Gavin project 2). We are trying to calculate splicing efficiency for all introns in S. pombe. I am seeking community help if anyone can guide me on how to obtain sequence reads for each intron and its flanking exons. Thank you in advance for the input and help !
maybe follow any published protocol/workflow. If you are after read counts in exons, maybe look at DEXSeq tools or use tools like featureCounts without aggregation of counts. To get sequences have a look at interval tools, such as bedtools. You also can get positions of introns using bedtools, if you have 12 columns BED files.