Sequencing results should be converted to datafiles with numbers of sequences mapped on each nucleotide in the reference genome. These files can be easily generated from indexed BAM files (mapping results) using the "genomeCoverageBed" tool available from the BEDTOOLS suite [1].
More information concerning file descriptions can be found online: http://bpeaks.gene-networks.net/.File format should be as follows (chromosome, position, number of sequences):
lll{
chrI 1chrI 2chrI 3chrI 4chrI 5chrI 6chrIchrI 8chrI 9chrI 10
dataReading(IPfile, controlFile, chromosomalFeatures = "")
- IPfile
{
Name of the file with sequencing results related to IP sample
}
- controlFile
{
Name of the file with sequencing results related to control sample
}
- chromosomalFeatures
{
Not mandatory. Name of the file with annotated positions of chromosomal features to use for peak location (see the function peakLocation for more details)
}
To obtain a required file from a BAM file (resultFile.bam), the command line is (SHELL):
genomeCoverageBed -ibam resultFile.bam -d > resultFile.txt
More information concerning file conversions can be found online: http://bpeaks.gene-networks.net/.
A list with three elements ($IPdata, $controlData, $chromosomalFeatures): IP data, control data and (if specified by user) chromosomal features for locations of peaks.
[1] Quinlan AR and Hall IM, 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 26, 6, pp. 841 842.
[object Object]
Conversion of file formats regarding sequencing results can be a tricky task. Detailed information can be found online http://bpeaks.gene-networks.net/. Don't hesitate to contact us for further discussions.
peakLocation
dataPDR1
# get library
library(bPeaks)
# Sequencing result files associated to PDR1 datasets (IP and control files)
# can be downloaded from our website http://bpeaks.gene-networks.net/.
# They are respectively named "IP_genomeCoverage.txt" (IP sample) and
# "INPUT_genomeCoverage.txt" (control sample).
# Import in R the sequencing results (no file for chromosomal features
# is specified here)
seqResult = dataReading("IP_genomeCoverage.txt", "INPUT_genomeCoverage.txt")
# IP data
seqResult$IPdata
# control data
seqResult$controlData
# run peak detection from IP and control data (with default parameters)
bPeaksAnalysis(IPdata = seqResult$IPdata, controlData = seqResult$controlData)
data reading