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RajLabMSSM / QTL-mapping-pipeline

A snakemake pipeline for QTL mapping. Based on the GTEX pipeline
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map_junctions_to_genes #5

Closed jackhump closed 4 years ago

jackhump commented 4 years ago

  1. does not take strand into account - this is obvious.

  2. should be run downstream of junction filtering to avoid mis-classifying a cluster

  3. if multiple genes overlap junctions in a cluster, which gene is picked as the name?

jackhump commented 4 years ago

reduce the chance of (3) by reducing maximum intron length - will remove some long-range spurious junctions that connect two genes (probably due to cross-mapping).

jackhump commented 4 years ago

hmm, now it's throwing out my junctions because of stranding mismatches. what to do?