README.md

Introduction

nf-core/lncinference is a bioinformatics pipeline that is suitable for transcript imputation of bulk RNA-seq from Oxford Nanopore sequencing.

1. Reads QC (FastQC and Nanoplot)
2. Reads filtering (Optional - Nanofilt)
3. Present QC before and after filtering for raw reads (MultiQC)
4. Align reads against a reference genome (Optional - Minimap2)
5. Extract gtf file from alignment (Stringtie)
6. Extract fasta from gtf produced by the last step (gffread)
7. Predict coding potential of transcript present in fasta file (RNAmining)

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

In the case of single end data:

samplesheet.csv:

sample,fastq_1,fastq_2
CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,
CONTROL_REP2,AEG588A2_S1_L003_R1_002.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 nf-core/lncinference \
   -profile <docker/singularity/.../institute> \
   --input samplesheet.csv \
   --outdir <OUTDIR>

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 and the parameter documentation.

Pipeline output

To see the results of an example test run with a full size dataset refer to the results tab on the nf-core website pipeline page. For more details about the output files and reports, please refer to the output documentation.

Credits

lfreitasl/lncinference was originally written by Lucas Freitas.

We thank the following people for their extensive assistance in the former analysis development of this pipeline: Bárbara Borges Laura Shimohara

Contributions and Support

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

For further information or help, don't hesitate to get in touch on the Slack #lncinference channel (you can join with this invite).

Citations

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

You can cite the nf-core publication as follows:

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.