mskcc/forte

Introduction

mskcc/forte is a best-practice analysis pipeline for bulk RNAseq.

• Functional
• Observation of
• RNA
• Transcriptome
• Elements/Expression

Features

1. Read pre-processing
   1. Trimming
   2. UMI extraction and deduplication
2. Alignment
3. Transcript quantification
4. Fusion calling and annotation
5. FASTQ and BAM QC
6. Fillouts

Usage

Note

If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow.Make sure to test your setup with -profile test before running the workflow on actual data.

First, prepare a samplesheet with your input data that looks as follows:

samplesheet.csv:

sample,fastq_1,fastq_2
CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz

Each row represents a fastq file (single-end) or a pair of fastq files (paired end).

Now, you can run the pipeline using:

nextflow run /path/to/clonedrepo/main.nf \
  --input samplesheet.csv \
  --outdir <OUTDIR> \
  --genome GRCh37 \
  -profile singularity

Warning

Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs.

For more details and further functionality, please refer to the usage documentation.

Credits

mskcc/forte was originally written by Anne Marie Noronha [email protected].

We thank the following people for their extensive assistance in the development of this pipeline:

• Allison Richards [email protected]
• Alexandria Pinto [email protected]
• Yixiao Gong [email protected]

We also thank the following contributors:

• Sam Tischfield [email protected]
• Martina Bradic [email protected]
• Jun Woo [email protected]
• Mark Donoghue [email protected]
• Helen Won

Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines.

Citations

An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.

This pipeline uses code and infrastructure developed and maintained by the nf-core community, reused here under the MIT license.

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.