Runs the SUPPA2 software after recommended data processing of fastq files.
- This pipeline is based on nextflow. As we have several nextflow pipelines, we have centralized the common information in the IARC-nf repository. Please read it carefully as it contains essential information for the installation, basic usage and configuration of nextflow and our pipelines.
- External software:
- trimgalore
- salmon
- SUPPA2
You can avoid installing all the external software by only installing Docker. See the IARC-nf repository for more information.
| Type | Description |
|---|---|
| input_folder | Folder containing fastq files to be aligned |
| input_file | Input file (tab-separated values) with 4 columns: ID (sample name), RG (read group), pair1 (first fastq pair file), and pair2 (second fastq pair file) |
| Name | Example value | Description |
|---|---|---|
| index | salmon_index | Reference fasta file (with index) for splice junction trimming and base recalibration |
| gtf | GRCh38_gencode_annotation.gtf | Path to annotation gtf file |
| Name | Default value | Description |
|---|---|---|
| output_folder | RNAsplicing-nf_output | Output folder' |
| cpu | 4 | Number of cpu used by salmon (default: 4).' |
| mem | 10 | Size of memory used for mapping (in GB) ' |
| fastq_ext | fq.gz | Extension of fastq files ' |
| suffix1 | 1 | Suffix of fastq files 1' |
| suffix2 | 2 | Suffix of fastq files 2' |
| mem_QC | 2 | Size of memory used for QC and cutadapt (in GB)' |
| cpu_trim | 15 | Number of cpu used by cutadapt ' |
| index | salmon_index | Path to salmon index folder' |
| suppa_folder | SUPPA | Path to SUPPA folder (cloned from github) containing suppa.py and folders scripts.' |
| ioe | null | Path to SUPPA ioe file. If not specified, will generate the file.' |
nextflow run iarcbioinfo/RNAsplicing-nf --input_file input.tsv --index salmon_index --gtf annot.gtf
| Type | Description |
|---|---|
| QC/adapter_trimming | Fastqc reports from trim_galore |
| quantification | Transcript expression quantification from salmon |
| results/*ioe and ioi files | SUPPA2 ioe and ioi files used for quantification of psi by events and isoforms |
| results/psiPerEvent | Files with psi per event for each sample |
| results/psiPerIsoform | Files with psi per isoform for each sample |
Nextflow pipeline that implements the SUPPA2 tutorial, first running salmon for quantification, then postprocessing the salmon outputs, creating the SUPPA2 ioe and ioi files if necessary, and computing psi per event and isoform for each sample.
| Name | Description | |
|---|---|---|
| Nicolas Alcala* | alcalan@iarc.who.int | Developer to contact for support |
| Ricardo Blazquez Encinas-Rey | Developer |
- Trincado JL, Entizne JC, Hysenaj G, Singh B, Skalic M, Elliott DJ, Eyras E. SUPPA2: fast, accurate, and uncertainty-aware differential splicing analysis across multiple conditions. Genome Biol. 2018 Mar 23;19(1):40.
- Alamancos GP, Pagès A, Trincado JL, Bellora N, Eyras E. Leveraging transcript quantification for fast computation of alternative splicing profiles. RNA. 2015 Sep;21(9):1521-31.