riboseq-flow results for OTTR ribo-seq data in human cells from Ferguson et al., 2023

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

Underlying data for Use case I 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 293T cells from Ferguson et al., 2023 with riboseq-flow. 

Raw FASTQ files processed are available from the NCBI Short Read Archive under accession no. SRP419250. Below are the SRA accession codes, experiments and descriptions: 

• SAMN32928155: nuclease digestion of biological replicate 1 of 293T cell lysate with RNase I (hR1 - SRX19188681).

• SAMN32928156: nuclease digestion of biological replicate 2 of 293T cell lysate with RNase I (hR2 - SRX19188682).

• SAMN32928153: Nuclease digestion of biological replicate 1 of 293T cell lysate with P1 nuclease (hP1 -SRX19188679).

• SAMN32928154: nuclease digestion of biological replicate 2 of 293T cell lysate with P1 nuclease (hP2 - SRX19188680).

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.

• results.zip: results produced by riboseq-flow
• Ribo-seq_multiqc_report.html: MultiQC report summarising read and mapping statistics, and ribo-seq quality control metrics.