SEmRNA-seq-nf

A Nextflow pipeline used for quantification and quanlity control for single-end RNA-seq data of C. elegans.

Usage

Clone this pipeline use command below to quest:

git clone https://github.com/gaotian52/SEmRNA-seq-nf.git

and cd SEmRNA-seq-nf

nextflow kallisto_SE.nf --fqs=test.tsv

Pipeliine parameters

• --fqs

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

Each column represent strain_name sample_name raw_FASTQ Note that sample_name should be unique for each sequence.

• --ref

Reference genome. Default = c_elegans.PRJNA13758.WS276.genomic.fa.gz

• --vcf

Variant Call Format (VCF) file. Default = WI.20200815.hard-filter.vcf.gz

• --gff3

GFF3 file. Default = c_elegans.PRJNA13758.WS276.annotations.gff3.gz

• --out

Used to specify the output directory. Default = "RNAseq_SE-${date}"

• --fragment_len

Estimated average fragment length. see the kallisto document for details. Default = "70"

• --fragment_sd

Estimated standard deviation of fragment length. see the kallisto document for details. Default = "50"

• --bootstrap

Number of bootstrap samples used by kallisto. Default = "100"

Output

This pipeline will generate two folders, kallisto and multiqc_report in your working directory.

kallisto/: RNA-Seq mapping results

multiqc_report/:

 
├── multiqc_pre_trim_fastqc.html  # Summary of FastQC results on raw FASTQ files
├── multiqc_post_trim_fastqc.html  # Summary of FastQC results on FASTQ files trimmed by fastp
└── multiqc_kallisto.html  # Summary of kallisto log

Dependencies

• Nextflow

• bcftools

• gffread

• fastp

• Kallisto

• FastQC

• Multiqc