Motif Enrichment

[kopardev]

• [x] Get scripts from Khanlab ... append to pipeline
• [ ] Explore applicability of existing MOTIF enrichment rules/scripts from CCBR ChipSeq and ASAP pipelines

[kopardev]

Check out https://github.com/CCBR/ASAP/blob/master/workflow/scripts/ccbr_atac_motif_enrichment.bash

[slsevilla]

Hsien Chao’s chipseq pipeline code: https://github.com/CCRGeneticsBranch/khanlab_pipeline/blob/master/rules/pipeline.chipseq.smk

Rules needed for annotation of carlisle output files

• rule peakAnnotation
• rule rose
• rule findMotif
• localrule prepareRoseSummit

localrule prepareSummit is NOT needed. It is used to remove blacklist or unused chromosomes, which is done in upstream steps of carlisle pipeline.

Probably it is easier to code separately for macs2 output and seacr output from carlisle pipeline.

[slsevilla]

rule peakAnnotation implemented - split into macs2 and seacar/gopeaks

[slsevilla]

rule rose and localrule prepareRoseSummit merged - complete for macs2

[slsevilla]

all rules are preliminary added - waiting for Yue to provide reference files and script files needed to complete motif analysis

https://github.com/CCRGeneticsBranch/khanlab_pipeline/blob/master/rules/pipeline.chipseq.smk https://github.com/CCRGeneticsBranch/khanlab_pipeline/blob/master/config/chipseq.yml

[slsevilla]

Test run in progress- all annotation files have been added

[slsevilla]

Update ROSE to v1.3.1 - Biowulf has added module

[slsevilla]

Updated code to rose expected output. running test with samples now Dry-run was successful .... submitting jobs to job-scheduler Running... 56996459

[slsevilla]

rule successfully implemented in pipeline