I was performing RNAseq analysis on Galaxy. I already used trimmomatric on my fastq files and would like to perform the STAR RNA mapping with the files generated after using trimmomatic. I was wondering if this is alright? Cause I tried to do this on one of my samples and it returned an error. Also, is it possible to run the STAR RNA parameters on all samples at once?
Thank you for this really good platform and I really look forward to your response.
If you don’t have reference annotation yet for the mm10 genome, there are a few choices. One is UCSC in their downloads area (not from the Table Browser). Navigate to the file, then copy the URL and paste it into the Upload tool. This prior Q&A explains how to do this for another genome – but the method is mostly the same for any genome. You want mm10.
I added a few tags to your post that point to more Q&A. Genecode is another common annotation source for this genome build/version – just be aware that from that source you’ll need to remove the headers before using the dataset (this can be done is Galaxy, as explained in other posts).
Hi @s.godbole Looks good! And yes, you need to enter the URL for exact files, not URLs for directories containing files. Apologies if that wasn’t clear! The intention was to offer a general pointer for where to look (directory structures are a bit complicated – plus many genomes have more than one GTF choice). RefSeq is certainly a good pick for mouse