Plz add built-in reference genome of domestic water buffalo.
Hello @rkd
Please try using the Custom Genome function to load your reference genome and paired annotation into Galaxy. This will work at any server and works just like a native reference genome.
Instructions are here for the genome → FAQ: How to use Custom Reference Genomes?
Then, for reference data, this guide explains how to make sure the content will work with most (all?) tools. The examples are for transcriptomics tools but single cell and variation tools mostly expect the same content → FAQ: Extended Help for Differential Expression Analysis Tools
For an example of retrieving similar data, please see
- from NCBI → Inquiry about lettuce genome
- from UCSC → Correct reference transcriptome for Salmon quant on existing RNASTAR alignments
- more general help → Using the salmon tool I´ve got UCSC ids instead of gene_ids
Your genome appears to be available here from NCBI. This means the data retrieval and preparation would be the same as the lettuce example above. (I didn’t see it hosted by UCSC yet, but maybe looked in the wrong place?)
More examples can be found under custom-genome custom-build reference-genome reference-annotation reference-transcriptome
Please give this a try and let us know if you need more help or if you are able to get this working! 