How to get Cufflinks data for MISO alternative splicing events?

Question

[thefirstrealace]

Hello,

I am currently doing an analysis on splice junctions at alternative exons, that belong to exon-skipping (ES) events. Therefore I have done the following steps so far:

1. I downloaded mRNA-Seq reads from human spleen cells from GEO
2. I used TopHat to mao these reads to hg19
3. I used TopHats accepted_hits.bam file and an Ensemble gene annotation provided by the MISO homepage for transcript assembly and abundance estimation with Cufflinks
4. I used TopHats accepted_hits.bam file and an ES event annotation from the MISO homepage for detection and quantification of ES events with MISO

I now have the following data:

• assembled_transcripts.gtf file from Cufflinks containing for each transcript an ensemble gene ID, exons, FPKM and some other values
• misoresults.miso_summary file from MISO containing the ES events given as exon triplets and some properties for each ES event
• ES_to_ensGene_hg19.txt file containing Ensemble gene ID(s) for each ES event in the MISO summary file above

Now, for each ES event in the MISO summary file I need to have the FPKM, TSS and TTS of the respective transcript. Which tool(s) can I use for that task? I hope that somebody can help me with that.

Best regards