Sample Data for RiboFlow

All files and references herein are coming from the human genome.

The files in this repo are small subsets of the originally published data.

Required and Optional Files

Not all files are required by RiboFlow.

Fastq

1. Ribosome profiling with UMIs, plus matched RNA-Seq: (GSM8325903, GSM8325907 ribo; GSM8325891, GSM8325895 RNA-Seq). Sourced from NCBI GEO accession number GSE269734 published in Liu et. al. One .fastq.gz each containing preselected reads aligning to the shipped reference.

2. Bulk ribosome profiling and RNA-Seq data: (GSM1606107, GSM1606108 ribo; GSM1606099, GSM1606100 RNA-Seq). Sourced from NCBI GEO accession number GSE65778 published in Sidrauski et. al.

3. Paired-end RNA-Seq: fastq/rnaseq_pe/SRR1039508/ sourced from NCBI GEO accession number GSE52778 published in Himes et. al.

Annotation

The tsv file contains transcript lengths. The bed file contains region boundaries; CDS, 5'UTR and 3'UTR.

Metadata

Contains metadata for the ribo files in yaml format — GSM1606107.yml, GSM1606108.yml and ing_hek293.yaml, covering the GSE65778 samples.

Transcriptome Reference

Bowtie2 index files for the transcriptome. The actual output of the RiboFlow pipeline, i.e., ribo files, is obtained using the reads that are mapped to the transcriptome reference.

Filter

Bowtie2 index coming from the filter sequences which are mainly ribosomal and tRNAs.

Genome

genome/star_index/ — a prebuilt STAR index of human chrM.

input:
  reference:
    genome: ./rf_sample_data_genome/genome/star_index

See genome/README.md.

Genome Source

genome/genome_source/genome.{fa,gtf} — the uncompressed FASTA + annotation the index above was built from, currently chrM. example_build_index.yaml feeds them to the pipeline's build-from-FASTA path (Mode B, STAR --runMode genomeGenerate), which writes back to genome/star_index/:

input:
  reference:
    genome_fasta: ./rf_sample_data_genome/genome/genome_source/genome.fa
    gtf:          ./rf_sample_data_genome/genome/genome_source/genome.gtf