add contrast comparisons between peaks

[slsevilla]

• [ ] updating config to take in contrast.tsv
• [ ] create rules to run deeptools on samples (correlation matrix, heatmaps, profiles, summary)
• [ ] create rules to create counts matrix
• [ ] create rules to perform DESEQ between contrasts - output a diffresults.txt
• [ ] create rules to perform conversion of diffresults to bed file

[slsevilla]

ASAP dir already run:

[12:46 PM] Goldfarbmuren, Kate (NIH/NCI) [C] /data/NCI_VB/berzofsky/ccrvb16_2018invitroHuman_ATACseq_KCG/ASAP_221212/

[12:47 PM] Goldfarbmuren, Kate (NIH/NCI) [C] /data/NCI_VB/berzofsky/ccrvb16_2018invitroHuman_ATACseq_KCG/PostASAP_dev/

[kopardev]

I already have scripts for most of these. Let's talk next week. I don't want you to reinvent the wheel.

[slsevilla]

Plan counts matrix

• take output from atac_genrich_peakcalling_fixed_width :
  • renormalizedConsensusNarrowPeak=join(RESULTSDIR,"peaks","genrich","fixed_width","{sample}.renormalized.fixed_width.consensus.narrowPeak")
• run python script
  • python {params.pyscript} --bedbedgraph {input.inputs} --tmpdir $TMPDIR --countsmatrix {output.cm} --fragmentscountsmatrix {output.fcm} --sampleinfo {output.si}

plan differential:

• create config file with contrasts
• perform QC check - contrasts are in sample manifest
• run DESEQ on contrasts

[slsevilla]

Counts matrix: https://github.com/CCBR/ASAP/issues/17

[slsevilla]

http://genomespot.blogspot.com/2015/01/generate-rna-seq-count-matrix-with.html