lincoln-harris / mutations-v-coverage_inkling

lets look at the relationship between mutations and coverage

mutations-v-coverage_inkling

Lincoln Harris
CZ Biohub, January, 2019

I have a feeling that if i calculate the relationship between number of mutations and expression/coverage, something good will come of it.

Method

1. downsample dataset
   maybe all of the cells from 2 given clusters
2. calculate coverage, transcriptome wide (bedtools?)
   how much of this info do we already have, in vcf files?
3. select gene panel of interest
   start with EGFR and Actin, maybe
4. normalize expression/coverage across all samples, for GOI
   (FPKM?)
5. plot number mutations v. normalized expression grab mutation info from makeGeneCounts_parallel.py output (s3://darmanis-group/singlecell_lungadeno/non_immune/analysis/geneCellMutationCounts.csv)