How do i move ahead…Is there any built in reference genome available that I can just directly upload onto it (from ENSEMBL ?)
Hopefully we can help!
You can use a Custom Genome with any tool. All that is needed is a fasta file in your history.
- Custom genome + custom build: How to use a genome that is not natively indexed at the server you are working at - #2 by jennaj
- Then, see the Mapping step in this tutorial (or try it all, this is our primary introduction and is worth it!) → Hands-on: NGS data logistics / NGS data logistics / Introduction to Galaxy Analyses
Which fasta to choose has considerations.
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Choose the reference annotation at the same time (
gtforgff3file). Please be aware that some Bioconductor tools do not parse raw Ensembl identifiers (with version) well, and using a UCSC version that has been sanitized a bit can be easier. Or, you can remove the.Nparts of the accession yourself (from all files!) if an error or odd result comes up. -
Consider where you plan to visualize your data. IGV is available to all genomes, including custom genomes, but has a few extra steps to create the database key. If you sourced the data from UCSC instead, and used their version of the genome and annotation (including the Ensembl genes track), and assigned a native database key, then everything would be native in both IGV and and at UCSC.
More help at custom-genome custom-build reference-genome reference-annotation igv
Please give this a try a follow-up questions are welcome! 