For HISAT2 I am using the Rat fasta annotation file. Is it supposed to be any particular one? Also from UCSC? I don't remember where I downloaded it.
Thanks Andrew
Hello,
Please see "Method 6" in this FAQ for data provider choices (common choices, not all): https://galaxyproject.org/support/chrom-identifiers/#any-mixed-sourced-data
iGenomes does have a UCSC rn6 GTF reference annotation file that will work well with all tools. See the FAQ for where to get this and how to Upload the data to Galaxy.
Avoid UCSC's GTF if you can - the same value is populated for gene_id and transcript_id (both are the transcript name) in the Table Browser's GTF output. This means summaries and counts will all be "by transcript" instead of "by gene", even if labeled otherwise in the tool output.
If you have another follow-up question related to this, just post it here in this thread back as a comment and we can help more. Spreading this across multiple posts results in information disconnect during the troubleshooting.
Thanks! Jen, Galaxy team
