Hi, I am analyzing an infection time course in a human cell line transduced with Vaccinia virus. The Vaccinia virus genome is not available in genomes section. I used the instructions here (https://galaxyproject.org/learn/custom-genomes/) to download the Vaccinia virus genome (https://www.ncbi.nlm.nih.gov/nuccore/AY243312.1?report=fasta) (approx 195Kb genome). Normalized using the toolkit NormalizeFasta trimmed the first line and used this as my custom genome. I made this as a custom build and performed alignment using STAR with no success.
1) The same setup works fine with BWA alignment. Could someone give any insights?
2) Viral genomes have no chr contig references. Is there anyone who has used a viral genome as a custom genome. Can anyone let me know how to proceed with the chromosome coordinate formatting for RNA STAR alignment?
3) How do you append Viral genome to the human genome and merge human and viral GTF/GFF files?
Thanks for your help/advice, anything that would involve galaxy tools for manipulation would be a plus. Cheers Nambi