README.md

INK-SQUID

Interpreting novel and known sQTLs underlying isoforms in diseases

Documentation

The steps for each tasks performed in the tool are broken down into the following.

1. A_SNP_junction_set
2. B_SNP_donor_acceptor_set
3. C_overlap_set

Input Data

• Sample MTCL1 datasets are provided in the /data directory.
• Toy GTF annotation file can be downloaded from Biosurfer Zenodo (link) or by clicking here.

The included MTCL1 example can be run with the following base command:

python3 main.py data/MTCL1/MTCL1_QTL_results.tsv data/MTCL1/MTCL1_moloc_results.tsv data/gencode_toy/gencode.v38.toy.gtf