(Not uploaded)

From Flybase:

• Dmel all GFF 6.35
• Dmel all GTF 6.35
• Dmel genome fasta 6.35
• tRNA fasta 6.35

From Ribogalaxy:

• rRNA fasta

Sequencing data:

• Small polysome footprints RPF sample

• subsampled fastq (head -400000 SRR1548656.fastq > SRR1548656_subsample.fastq)
• Fasta and gff - formatted for Riboviz
• Filtered fasta and gff - one CDS per gene

• Converting fly genome - script to make ORFeome GFF and fasta from flybase reference GFF and fasta.
• Filtering fly genome - script to filter ORFeome GFF and fasta to one (longest) CDS per gene.
• Outputs in Processed data
• Needs update. Test mouse genome - successful test on mouse gencode reference genome.
• Needs update. Test yeast genome - as yet unsuccessful test on yeast reference genome - needs fasta header editing step, and genome padding. Likely to be needed for any non-standard annotations.

Test running converted filtered fasta and gff on Riboviz. Includes params file, output from checks, etc.

Check gff: python -m riboviz.tools.check_fasta_gff -f /Users/isabelbirds/Documents/GitHub/Drosophila_Riboviz_work/2_Processed_data/Dmel/Dmel_filtered.fasta -g /Users/isabelbirds/Documents/GitHub/Drosophila_Riboviz_work/2_Processed_data/Dmel/Dmel_filtered.gff3 -o /Users/isabelbirds/Documents/GitHub/Drosophila_Riboviz_work/4_Riboviz_test/Dmel_filtered.issues.tsv --use-feature-name -v

Validate config: nextflow run /Users/isabelbirds/Documents/Programs/Riboviz/riboviz/prep_riboviz.nf -params-file Aspden_2014_RPF_config.yaml --validate_only

Run riboviz: nextflow run /Users/isabelbirds/Documents/Programs/Riboviz/riboviz/prep_riboviz.nf -ansi-log false -params-file Aspden_2014_RPF_config.yaml