Introduction

nf-core/finalproject is a bioinformatics pipeline that aims to analyze RNA-Seq data when there is a necessity for a filtering step. It is useful when the RNA-Seq experiment was performed in cell culture or by another design where there is a high probability of contamination of the target transcriptome with the host transcriptome.

1. Read QC (FastQC)
2. Align reads against the host organism genome and select reads that do not align (Bowtie2)
3. Align reads against the target organism genome.
4. Present QC for raw reads and the alignments (MultiQC)

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 iaradsouza1/finalproject \
   -profile <docker/singularity/.../institute> \
   --input samplesheet.csv \
   --outdir <OUTDIR> \
   -revision master

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, please refer to the usage documentation and the parameter documentation.

Pipeline output

To see the results of a 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

nf-core/finalproject was originally written by Iara Souza.

Contributions and Support

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

Citations

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.