Workflows

Quality control, alignment, filtering, and track creation

Each assay-named workflow does the following general steps: \

1. Adapter trimming and Quality Control checks with FastQC.
2. Alignment to a reference genome (STAR for RNA, BWA mem for ChIP/ATAC)
3. Multiple rounds of filtering after alignment:
   • Remove scaffolds (keep list of cannonical chromosomes in chromNoScaffold input parameter
   • Mark and remove duplicate alignments
   • Remove unmapped alignments
   • Conditionally remove blacklisted regions, if such a file is supplied to the blackList input parameter
   • Sort and index the final bam.
4. Produce normalized (TPM) track (bigWig) files

READMEs in each of the subdirectories outline parameters, steps, and outputs of each workflow.