Hi everybody, i was asking how select a reference genome different to that already present in the option of RNA STAR. Thank you for your help!
Hi,
If I understand it correctly, you want to use a genome fasta file that is not available as a built-in genome. If that is the case, you can change Custom or built-in reference genome to use reference genome from history and create temporary index option. Then, using the Select a reference genome, you should select the genome file that you have already uploaded to your history. It should be either fasta or fasta.gz format.
If you have a gene model for your genome of interest, you can also include that using the following option: Build index with or without known splice junctions annotation and setting it to build index with gene-model. Here, again you should select your gene model (gtf or gff3 format) from the history.
Of course, there are multiple other options that you can use to index the genome of interest based on the settings that you are interested in.
Best,
Armin