(WP4) Script to summarize splice junction reads to produce BED file

[haessar]

There are existing tools that will take a BAM file and output a BED with read count in the score column (see e.g. regtools).

I want to adapt this to also assign a itemRgb column with different predefined RGB values for a series of cell type mappings, and also rescale the score column to have a maximum value of 1000.

[FrancesBlow]

regtools_bed_by_celltype.py takes a bam file that has been split into separate bam files by cell type, runs regtools to output a BED with read count in the score column, edits the rgb column in each resulting bam file to have a different colour per bed/celltype, and concatenates the bed files together.

[FrancesBlow]

Still to do: scale the number of reads supporting each junction to 1000 per gene

• Group entries in the resulting merged bed file by gene, probably using gene annotations from the gff (maybe using bedtools intersect?)
• Scale the read counts in the 'score' column (5th column in BED12 output from regtools) to 1000 for each gene

[haessar]

I've merged the PR #21 but will leave this open for the TODOs.

[FrancesBlow]

Additional to do:

• Sort the list of bam files alphabetically before assigning a RGB colour to them, in the hope that similar cell types are assigned similar colours on the colour wheel