Man pages for UvA-MAD/faradr
Tools for sequencing data analysis.
| A.design.plot | Plot number of reads in each sample for each grouping factor. |
| Aplot | Plot number of reads in each sample. |
| B1.design.plot | Plot read lenght distribution |
| B1plot | Plot read lenght distribution |
| B2.design.plot | Plot fraction of reads with particular lengh or longer. |
| B2plot | Plot fraction of reads with particular lengh or longer. |
| C1.design.plot | Plot mean read quality distribution per sample. |
| C1plot | Plot mean read quality distribution per sample. |
| C2.design.plot | Plot mean base quality at particualar position in the read. |
| C2plot | Plot mean base quality at particualar position in the read. |
| C3.design.plot | Plot fraction of reads with partucular quality or higher per... |
| C3plot | Plot fraction of reads with partucular quality or higher per... |
| CombineCountTables | Plot number of reads in each sample for each grouping factor. |
| CountTable | Count reads in all |
| D1plot | Plot base frequnecy for first 30 nt. |
| D2plot | Plot base frequnecy for last 30 nt. |
| GeneralQualityStats | Get quality statistics. |
| normalize_counts | Normalise counts based on normalisation spike counts |
| PlotAlignAnnot | Plot aligned reads over annotated region. |
| PlotCoverageAnnot | Plot aligned reads over annotated region. |
| PlotMeanReadQuality | Plot mean quality per read |
| PlotMMDist | Plot distribution of mismatches and indels in alignment. |
| PlotMMFracDist | Plot fraction of mismatches and indels in alignment. |
| PlotNormalSpikeCounts | Plot normalised spike counts |
| PlotPerCycleQuality | Plot quality scores per cycle |
| PlotReadLengthDistribution | Plot read length distribution |
| PlotSpikeCounts | Plot spike counts |
| QualityTrimReads | Trim fastq reads. |
