I’m currently trying to use Kallisto quant to perform a quick and dirty abundance analysis of specific reads from RNAseq data for an organism who’s database is already included as a reference transcriptome on galaxy - Zostera marina JGI v2.2. However, whenever I try to run the raw fastqsanger.gx data, I keep on receiving the following error message -
Error: kallisto index file not found /data/db/data_managers/Zostera_marina_JGI_v2.2/kallisto_index/Zostera_marina_JGI_v2.2_all_tx_transcriptome/Zostera_marina_JGI_v2.2_all_tx_transcriptome
Would I be correct in assuming that Kallisto is struggling to use the build in reference transcriptome? is there anything I can do to rectify this?
Yes, the transcriptome indexes seem to be a problem at UseGalaxy.eu. I’ve reported it to the administrators.
Now, most public Galaxy servers never host trascriptomes at all since the annotation itself updates all the time, and that impacts the associated transcriptome fasta files. Plus there are versions of those files: all, primary only, maybe other rules you want to apply (no housekeeping and such).
It looks like the file you want is here at JGI. I don’t see a way to get to the data by publicly accessible URL but if they do offer it that way, you can paste the URL into the Upload tool. But maybe that site requires a download/local file browsing Upload step instead, you’ll need to check.
Or, you could get the version at NCBI from here in the FTP directory. That would let you get everything: genomic and annotation. You can parse out transcripts from the annotation with a tool like gffread, and limit which transcripts to report, or get all.
Once a fasta is in Galaxy, treat the data just as you would a custom genome. Data providers include all sorts of extra content – but informatics tools mostly want really simple formats, and Galaxy is just those original tools so the cleanup is still needed. So, simply the fasta format with the tool we recommend here. → FAQ: How to use Custom Reference Genomes?
Thanks for reporting the problem and I hope this gives you a few alternatives to try!
