Man pages for UvA-MAD/faradr
Tools for sequencing data analysis.

A.design.plotPlot number of reads in each sample for each grouping factor.
AplotPlot number of reads in each sample.
B1.design.plotPlot read lenght distribution
B1plotPlot read lenght distribution
B2.design.plotPlot fraction of reads with particular lengh or longer.
B2plotPlot fraction of reads with particular lengh or longer.
C1.design.plotPlot mean read quality distribution per sample.
C1plotPlot mean read quality distribution per sample.
C2.design.plotPlot mean base quality at particualar position in the read.
C2plotPlot mean base quality at particualar position in the read.
C3.design.plotPlot fraction of reads with partucular quality or higher per...
C3plotPlot fraction of reads with partucular quality or higher per...
CombineCountTablesPlot number of reads in each sample for each grouping factor.
CountTableCount reads in all
D1plotPlot base frequnecy for first 30 nt.
D2plotPlot base frequnecy for last 30 nt.
GeneralQualityStatsGet quality statistics.
normalize_countsNormalise counts based on normalisation spike counts
PlotAlignAnnotPlot aligned reads over annotated region.
PlotCoverageAnnotPlot aligned reads over annotated region.
PlotMeanReadQualityPlot mean quality per read
PlotMMDistPlot distribution of mismatches and indels in alignment.
PlotMMFracDistPlot fraction of mismatches and indels in alignment.
PlotNormalSpikeCountsPlot normalised spike counts
PlotPerCycleQualityPlot quality scores per cycle
PlotReadLengthDistributionPlot read length distribution
PlotSpikeCountsPlot spike counts
QualityTrimReadsTrim fastq reads.
UvA-MAD/faradr documentation built on June 3, 2017, 8:43 a.m.