Atlas QC work - Githubissues

lzamparo / embedding

Learning semantic embeddings for TF binding preferences directly from sequence

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Atlas QC work #17

Open lzamparo opened 6 years ago

lzamparo commented 6 years ago

Still need to do a bunch of work on the atlas, some peaks seem spurious

Convert bedgraph files to bigwig track files, for easier validation in IGV
Distribution of support underlying peak-rich genes;
- peak height re-scaled by library size
- total corrected coverage divided by peak length
Make bigwig tracks for combined replicates of each cell type, plot over atlas to see which peaks are being driven by signal in which CTs

lzamparo commented 6 years ago

I can repurpose code from the safe harbour project to do this, at least the bw track generation

lzamparo commented 6 years ago

Done, need to embed work from Google Sheet here. Upshot is that many peaks still show up which look spurious, but can pass even a very stringent IDR filter. Next steps to reduce number of spurious peaks could be:

Tighten threshold on meta-bam peak calling; might be allowing for too many regions that do not contain real peaks.
Might be that I have to apply a heuristic for rejecting low-coverage peaks post-hoc. Can look at the pan-celltype distribution of normalized peak heights genome-wide and the per-celltype distribution of normalized peak heights. Hopefully there is some modality to be observed, and sensible thresholds that can emerge.

lzamparo commented 6 years ago

Previous # peaks, IDR tournament (0.01)	New # peaks, IDR tournament (0.003)	Conservative # peaks, longest reproducible list (0.01)	Conservative # peaks, longest reproducible list (0.003)	Celltype

49759	41848	49056	41525	B cells
70710	59102	55060	48651	CD4+ T cells
70569	59514	64248	55644	CD8+ T cells
53975	45137	48195	41404	CLP
180499	151685	143887	123415	CMP
21214	18300	19444	16983	Erythroblasts
144310	122212	117925	101505	GMP
154618	134102	142287	126323	HSC
109981	94705	98020	85327	LMPP
141581	118702	132164	113193	MEP
55818	48647	51187	45740	Monocytes
137018	117803	118257	103617	MPP
67788	57087	51818	45691	NK cells