Fixed error in readme
WIP draft of new plot - overlap with genes, exons, rRNA and MT
Added check for TS and BS counts in case of strand information error for bismark coverage plot
Moved stranded counts check to a more sensible place..
Update the defaults for --max_cov in bismark_coverage plots
WIP count_biotypes new plot work
Resolved conflicts. WIP count_biotypes new plot work
First additions for new package. Bash scripts to set off SLURM jobs for subsampling and cufflinks
Clean up whitespace, fix some bugs..
Fixed problem where I hadn't updated the time limit, so everything failed after an hour, giving random results. Jobs now have 2 days to complete
First commit of new plotting script for subsampled cufflinks reports
WIP: First draft of readme for subsampled gene counts. Not finished.
Tidied up bash scripts. Command line args, symlinks in subsampling and some other bits.
Added functionality to use read counts from cufflinks log on plot axis. Other tidying up and testing.
Readme updates.
Changed name of Subsampled Gene Observations in readme and directory
New script to count aligned reads in bam files. Updated plotting script to use this instead of the cufflinks processed transcripts (which was wrong)
Readme update, with example output for subsampled gene counts
Readme updates.
Removed internal var names as no-one is ever going to use them