Frequently asked questions

I don’t want/I can’t install it on my computer. Can I still use Ribotools without installing the package?

Yes, you can use a Docker or a Singularity container. Simply pull, and you’re done! See Installation for instructions. Example calls are also given in the user guide and tutorials.

I have alignments, can I use Ribotools?

The short answer is yes. The pipeline is designed to handle all steps from raw FASTQ files up to the final count tables, but you can start the pipeline from any step. Check the Rp-Bp tutorial on how to use existing alignment files.

I have count tables, can I use Ribotools for TE/DE only?

Yes, check General workflow (TE) or General workflow (DE).

Can I quality control (QC) my data?

For Ribo-seq, Ribotools estimates periodicity by default, so you know which samples and read lengths are usable for downstream analyses. If you use Rp-Bp to create index files and run the pipeline with the --create-orf-profiles option, you can use the Rp-Bp profile construction dashboard to facilitate visualization and QC of your Ribo-seq data. See Ribo-seq quality control for more details. For RNA-seq, there are already plenty of QC tools.

I called run-htseq-workflow with the --run-all flag, why are there no RNA count tables?

If one of your Ribo-seq sample failed to complete, e.g. due to low quality (no periodic reads were found), all RNA samples will fail to run. In such cases, you can try to troubleshoot the problem by looking at the logs. You can decide to drop failed samples, or use fixed lengths and offsets, and re-run the workflow. The pipeline will skip existing files and continue were it failed, unless you use the --overwrite flag. This behavior may be different whether you are running samples sequentially or in parallel, e.g. with the --use-slurm option.

For TE/DE estimation, I get errors about undefined columns or NA values

If you get errors such as undefined columns selected, Error in DESeqDataSet: NA values are not allowed, or Gene IDs (first column) differ between files, this is generally due to not specifying --orfCol, --symbolCol, and/or the correct --delim for the count table. Check Estimate TE or DE using Ribo-seq ORFs for some hints.