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5 Tools supported
| Mapper | Option name (mapper) |
| BWA | bwa1 |
| BWA | bwa2 |
| Bowtie 1 | bowtie1 |
| Bowtie2 | bowtie2 |
| GEM | gem |
| GSNAP | gsnap |
| MapSplice | mapsplice |
| OSA | osa |
| SMALT | smalt |
| SOAPsplice | soapsplice |
| STAR | star |
| TopHat 1 | tophat1 |
| TopHat 2 | tophat2 |
| HISAT2 | hisat2 |
More information about the different mappers and links to the respective websites may be found here. Some mappers (e.g., mapsplice) may not be installed by default. The installation script may be used to install these mappers by using the -x option. For instance, the following command would try to install MapSplice in the existing iRAP installation
irap_install.sh -s change_to_path_to_irap_source_folder -x mapsplice
| Quantifier | Option name (quant_method) |
| Cufflinks 1 (do not assemble novel transcripts/-G) | cufflinks1_nd |
| Cufflinks 1 (try to find novel transcripts/-g) | cufflinks1 |
| Cufflinks 2 (do not assemble novel transcripts/-G) | cufflinks2_nd |
| Cufflinks 2 (try to find novel transcripts/-g) | cufflinks2 |
| FluxCapacitor | flux_cap |
| HTSeq (intersection non-empty mode) | htseq2 |
| HTSeq (union mode) | htseq1 |
| Kallisto | kallisto |
| NURD | nurd |
| RSEM (only works with STAR aligner) | rsem |
| StringTie | stringtie |
| Salmon | salmon |
| DEXSeq | dexseq |
| BitSeq | bitseq |
| FeatureCounts | featurecounts |
| umis | umis |
| umi_count | umi_count |
Exon level quantification can be enabled by defining the parameter exon_quant_method (e.g., exon_quant_method=dexseq). Currently the only exon quantification methods supported are StringTie, DEXSeq, FeatureCounts.
Unique molecular identifiers (UMI) counting methods supported: umis and umi_count.
| Method | Option name (de_method) |
| Cuffdiff 1 | cuffdiff1 |
| Cuffdiff 2 | cuffdiff2 |
| DESeq | deseq |
| DESeq2 | deseq2 |
| EdgeR | edger |
| VOOM | voom |
| EBSeq | ebseq |
Transcript level differential expression method may be selected by defining the parameter transcript_de_method.
Exon level differential expression method may be selected by defining the parameter exon_de_method (currently on dexseq is supported).
| Tool | Option name (gse_tool) |
| Piano | piano |
Although [[http://www.bioconductor.org/packages/release/bioc/html/piano.html] [Piano]] is the only tool supported, it includes several methods that may be used: mean, median, sum, fisher, stouffer, tailStrength, wilcoxon, reporter, and page. Nothe that “fisher-exact” test is also available (although is not part of Piano). For information about these methods and Piano we refer to the Piano documentation available here. More information about how to enable GSE analysis in iRAP is provided here.
| Tool | Option name (fusion_method) |
| FusionMap | fusionmap |