Yarden Katz
Yarden Katz
A feature that I'd find very useful is parsing of gffutils GFF records into a (lightweight) Gene-like object. Something like: ``` # recs is a set of GFF records gene_obj...
That identifies: 1. Current MISO installation 2. Default settings file 3. Python version that is used. 4. tagBam if there optionally
More aggressive error checking for procedures calling `tagBam` and processing its output
""" miso_zip.py does not work for Ensembl style chromosome titles. I think this is because sql tables cannot have integer names hence CREATE TABLE 11 (...) fails. I added an...
Re: request from UNC users.
Implement `--lazy` flag for running MAP estimate MISO in special case of single-end (no sampling, no BFs). Only outputs summary files.
Use kuler and/or equispacing (similar to ggplot2) to create default color schemes for sashimi plots. Make `colors` argument in settings file optional.
Fix up RPKM labels and give better vertical alignment of Psi tracks.
Switch to @daler 's gffutils from current hacky GFF parser. Find gene model abstraction that fits with minimal pain. Perform speed benchmarks between current parser and gffutils.
Add sanitized GFF annotations for events. Also offer annotations with introns. Reorganize annotations into systematic categories on separate page in manual and link to it. Clearly separate exon-centric and isoform-centric...