README.md

In damidseq/RDamIDSeq: DamID-seq pipeline (Adapter removal, Mapping to genome, analyzing)

RDamIDSeq

All in R DamID sequencing pipeline. Includes adapter removal, Mapping and enrichment finding for DamID-Seq reads.

For more information see also: Tools for DNA adenine methyltransferase identification analysis of nuclear organization during C. elegans development

install

1) Install R (only 64 bit version!) R Project

2) Download DamIDseq_0.1.3.tar.gz

3) install additional packages needed for the pipeline in R

install.packages(c('corrplot', 'aqfig')) source("https://bioconductor.org/biocLite.R") biocLite() biocLite(c("QuasR", "ShortRead", "GenomicRanges", "S4Vectors", "IRanges", "BiocInstaller", "Biobase", "Biostrings", "BSgenome", "GenomicFeatures", "GenomicAlignments", "BiocParallel", "GenomeInfoDb", "rtracklayer", "GenomicFiles", "Rbowtie"))

4) install DamIDSeq in R (exchange PATH with the path to the installation file on your disk)

install.packages("PATH/DamIDseq_0.1.3.tar.gz", repos = NULL, type = "source")

damidseq/RDamIDSeq documentation built on May 14, 2019, 3:33 p.m.