MR1

This repository contains scripts that reproduce a plot of the distributions of MR1 exon 4 inclusion-to-skip ratios across GTEx tissues starting Snaptron queries. Refer to query_and_generate_table.sh for how the queries were generated. The MR1 transcript NM_001531 includes exon 4 and is distinguished by two junctions, the average of whose coverages we call A; NM_001195000 excludes exon 4 and is distinguished by one junction, whose coverage we call B. query_and_generate_table.sh outputs isoform_ratio_table.tsv, which lists for each GTEx sample our proxy A / B for the isoform ratio as well as corresponding tissue labels. The notebook plots.nb generates the final plot histogramDensityPlot.pdf from isoform_ratio_table.tsv. We ran it with Mathematica 10.4.1 and saved a PDF transcript as plots.pdf.