nf_ccle's Introduction

nf_ccle

about

some info about the data: https://www.ebi.ac.uk/biostudies/files/E-MTAB-2770/E-MTAB-2770.idf.txt

To run

# start a tmux / screen session

module load nextflow

nextflow run main.nf -c ccle_params.config -resume -with-dag flowchart.mmd

Analysis steps

Using (https://github.com/samleenz/nf_modules) for analysis code

Quality control
- fastqc
- multiQC
Read Processing
- Trimming with cutadapt
Alignment
- STAR two-pass alignment
Quantification
- featureCounts

Versions

Ensembl release 108 for txome

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samleenz / nf_ccle Goto Github PK