amarinderthind / isotope

ISOform-guided prediction of epiTOPEs in cancer

ISOTOPE

ISOform-guided prediction of epiTOPEs in cancer

The following pipeline have been developed for the identification of cancer-specific splicing-derived epitopes from RNA-seq.

The pipeline is divided in 4 parts, depending the event type the user wants to obtain:

• Pseudoexons (Exonizations)
• New exons skipping events (Neoskipping)
• Alternative splice site (A5_A3)
• Intron retention (IR)

For the obtention of exonizations, neoskipping and A5_A3 events, the first input are the read counts mapped to all posible junctions in the genome. This file (readCounts.tab) is created through Junckey (https://github.com/comprna/Junckey#1-format-star-output). From these junctions, ISOTOPE will obtain all splicing events expressed significantly.

For the identification of IR events, a normalized expression like TPMs for all possible intronic regionic is needed. To this end, we first created a transcriptome with all possible intronic regions using kma (https://github.com/pachterlab/kma). By using a pseudoalligner like Salmon (https://combine-lab.github.io/salmon/) or Kallisto (https://pachterlab.github.io/kallisto/about) the quantification to these regions could be applied. With these values, ISOTOPE will filtered out intron retention events lowly expressed.

The workflow is quite similar between all event types, but there are some specificities important to take into account

The user must run each of the 3 parts sequentially. The scripts are ready to be run in a slurm cluster. Until all jobs generated by a part are finished do not run the following part. For the moment, the user needs to manually change in the code the input files. In the near future we will addecuate the pipeline for entering the files by command.

For any query related with the tool, please create an issue in the repository.