Man pages for BMILAB/scAPAtrap
Identification and Quantification of Alternative Polyadenylation Sites from Single-cell RNA-seq Data
| convertAPAtrapData | Convert the scExpMa list generated by scAPAtrap to other... |
| countPeaks | Calculate the expression level of each peak in each cell with... |
| dedupByPos | Deduplication with umitools |
| extractBcAndUb | Extract barcode and UMI in reads with umi_tools |
| findPeaks | Perform peak calling on a BAM file |
| findPeaksByStrand | Perform peak calling on a BAM file with single strand |
| findTails | Find the positions with polyA tails genome/chromosome-wide |
| findTailsByPeaks | Find tail positions around/within peak ranges |
| findUniqueMap | Filter a BAM file to preserve unique mappings with samtools |
| generateAlignBam | Align the sequence to the reference genome with STAR |
| generateFinalBam | Generate a BAM file for called peaks with featureCounts and... |
| generateRefIndex | Build the reference genome index with STAR |
| generateSAF | Generate a peak annotation file |
| generatescExpMa | Generate single cell expression matrix |
| initScAPAtrap | Initiate scAPAtrap and check/set parameters |
| loadBpCoverages | Load a BAM file and calculate coverages of each position with... |
| reducePeaks | Reduce peaks number in a countsfile and/or peaksfile |
| scAPAtrap | Wrapper function for one-step running of scAPAtrap |
| separateBamBystrand | Separate BAM files by strand |
| setTools | Set tool names for running scAPAtrap |
| setTrapParams | Set the parameters for running scAPAtrap |
| TRAPFILES | TRAPFILES global variable |
| TRAP.PARAMS | Get parameters to run scAPAtrap |
