riboseq-flow results for ribo-seq data in human and mouse brain from Wang et al., 2020

Riboseq-flow: A streamlined, reliable pipeline for ribosome profiling data analysis and quality control

Extended data for Use case II example from the manuscript introducing riboseq-flow, a Nextflow DSL2 ribo-seq analysis pipeline, including all the outputs produced by analysing ribo-seq data in human and mouse brain from Wang et al., 2020 with riboseq-flow. 

Raw FASTQ files are available from ArrayExpress under accession E-MTAB-7247. Below are the accession codes and assay names for the ribo-seq samples used:

• ERR2812346: human_brain_ribo_1

• ERR2812347: human_brain_ribo_2

• ERR2812348: human_brain_ribo_3

• ERR2812382: mouse_brain_ribo_1

• ERR2812383: mouse_brain_ribo_2

• ERR2812384: mouse_brain_ribo_3

Raw FASTQ files were downloaded with nf-core/fetchngs v.1.10.1 using download_fastq.sh.

After download, they were analysed with riboseq-flow v1.1.1 (10.5281/zenodo.10558537) using run_riboseq.sh scripts in each folder for human and mouse, respectively.

• human_brain.zip: code to run riboseq-flow and the results produced for human brain data
• human_brain_Ribo-seq_multiqc_report.html: MultiQC report summarising read and mapping statistics, and ribo-seq quality control metrics for human brain data
• mouse_brain.zip: code to run riboseq-flow and the results produced for mouse brain data
• mouse_brain_Ribo-seq_multiqc_report.html: MultiQC report summarising read and mapping statistics, and ribo-seq quality control metrics for mouse brain data