Elementolab/ChIPseeqer Supplementary

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Supplementary tools

• Supplementary tools : Find distal peaks (peaks that are distant from known genes)
  • Use ChIPseeqerFindDistalPeaks

• Supplementary tools : Given a set of peaks, find closest genes
  • Use ChIPseeqerFindClosestGenes

• Supplementary tools : Extract (maximum/average) reads count for peak regions
  • Use ChIPseeqerGetReadCountInPeakRegions

• Supplementary tools : Extract/Merge columns from the .genes.annotated.txt file (after ChIPseeqerAnnotate)
  • Use mergeCSAnnotateGenesColumns

• Supplementary tools : Run PAGE with a list of genes
  • Use make_PAGE_input.pl

• Supplementary tools : Create density map and sort based on a list of genes/transcripts
  • Use make_sort_cdt_matrix

• Supplementary tools : Find peak matches with FIRE motif
  • Use Find_peaks_with_motif.pl

• Supplementary tools : Plot average read density profile in gene parts: promoters, first exon, first intron, all other exons, all other introns.
  • ChIPseeqerPlotAverageReadDensityInGenes

• Supplementary tools : Plot average peak numbers in gene parts: promoters, first exon, first intron, all other exons, all other introns.
  • ChIPseeqerPlotAveragePeaksNumberInGenes