SEmRNA-seq-nf

A Nextflow pipeline used for quantification and quanlity control for RNA-seq data.

Usage

Clone this pipeline use command below:

git clone [email protected]:AndersenLab/SEmRNA-seq-nf.git

and cd SEmRNA-seq-nf

For local run, if you installed docker, you can run the pipeline with conmmand:

nextflow run main.nf -with-docker -profile local

Else:

nextflow run main.nf -profile local

To run this pipeline on quest, please use command:

nextflow run main.nf -profile quest

main.nf and test.nf

The main.nf is the default setting for this pipeline that using a sample sheet as input. The sample sheet should strictly follow the format showed in test.tsv. Each column represent strain_name sample_name ID sample_order absolute directory sequence_folder sub_folder unique_lable Note that sample_name ID absolute directory uniq_lable should be unique for each sequence.

test.nf is an option for those who do not want to creat a sample sheet. test.nf reads the path for raw sequences directly.

They have no effect on results.

Pipeliine parameters

• --fqs

We use a sample sheet as the input of sequences here, see the example in test.tsv.

• --transcriptome

Transcriptome used for reads mapping. This pipeline use alignment-independent methods for quantification. Thus, we don't need map to genome.

• --output

Used to specify the output directory

• --fragment_len

This is only used for single-end reads by kallisto. Pair-end reads do not need to set this parameter. see the kallisto document for details.

• --fragment_sd

This is only used for single-end reads by kallisto. Pair-end reads do not need to set this parameter. see the kallisto document for details.

• --bootstrap

Number of bootstrap samples used by kallisto.

• --experiment

This is an important params for pipeline, see the reference format in experiment_info.txt. The style should be strictly followed.

--experiment <experiment_info>

• --email

Add your email with command

--emial < ...@...>

When the pipeline completed or broken, you can receive the notification from your email.

Output

This pipeline will generate a report.html and trace.txt in your working directory.

Below are major results under results/.

├── log.txt                 # Running information
├── multiqc_report.html     # A conbined quanlity control results
├── sleuth_object.so        # Quantification results, open it in R with sleuth package
└── transcriptome.index     # Index of transcriptome generated by kallisto

Dependencies

• Nextflow

• Kallisto

• Salmon

• Fastqc

• Multiqc

• Sleuth