Collection of java command-line utilities used in the Pugh Lab (Center for Eukaryotic Gene Regulation @ Penn State) and as part of the Chip-exo Galaxy flavor. Written by Will Lai.
(after cloning this repo):
cd cegr-tools;
ant makealljars;
The makealljars build target builds jar files for each of the tools described below, and outputs them into the build/dist directory.
Converts BAM data to ScIdx, the Strand-specific coordinate count format, which is used by tools within the Chip-exo Galaxy flavor. ScIdx files are 1-based.
The format consists of 5 columns: the chromosome, the position of the genomic coordinate, the number of tags on the forward strand, the number of tags on the reverse strand and the number of total tags on the position.
With pair-end reads, only the 5' end of READ1 will be used to create the ScIdx data file. Tools that use this format include GeneTrack and MultiGPS.
Produces a graphical representation of FASTA data with each nucleotide represented by a selected color.
Creates a histogram of inferred fragment size lengths from mapped paired-end sequencing data.
Creates a composite histogram of mapped sequencing tag 5' ends around a set of genomic coordinate points.
Creates a cross-plot from paired end sequencing data.
Filters sorted and indexed BAM file by the -1 5' nucleotide given BAM file and genomic FASTA file