Elementolab/ChIPseeqer Dev Tips

From Icbwiki

Jump to: navigation, search

Development and maintenance tips for ChIPseeqer framework

Adding new gene annotations

Download the UCSC track and run script:

make_gene_annotation_files.pl --annotation=ChIPseeqer/DATA/mm9/acembly.txt.mm9.JUL2007

Files that are affected and need to be modified:

CSAnnotate
CSFindClosestGenes
CSFindDistalPeaks
CSSummaryPromoters
CSDensityMatrix
ChIPseeqerGetReadDensityProfilesForTranscriptList
CSiPAGE
ChIPseeqerPlotAverageReadDensityInGenes

Remember to put gene annotation files to the appropriate genome folder (e.g., hg18/, mm9/, dm3/)

Personal tools