RNA STAR error on trimmomtaic files

Hello Galaxy Community,

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.

Thank you again,

Best,
Shweta

Hi @s.godbole,
yes, this is fine. Could you share a screenshot of the error report? You can find it by clicking in the bug icon.

Regards

Hey @gallardoalba ,

Thank you for your response, I have put the file to run again now, if any error pops up then I will send a screenshot :slight_smile:
Also, Could you please tell me how could I run mapping on all my files please?

Thank you once again,

Best,
Shweta

I recommend you to have a took at this trainings; it explains how to create Collections, which is probably what you need:

Regards

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Dear @gallardoalba ,
I have attached the image for the error I encountered.

Best,
Shweta

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Hi @s.godbole

This error can be produced when options that require reference annotation are used, but no reference annotation is input.

Most likely, it was the option for Per gene/transcript output.

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).

Hope that helps!

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Dear @jennaj ,

Thank you very much for this input, I had completely forgotten about the gtf file, however, it did not like the input
Index of /goldenPath/mm10/bigZips/genes
so I put in very specific file input “http://hgdownload.soe.ucsc.edu/goldenPath/mm10/bigZips/genes/mm10.ncbiRefSeq.gtf.gz”. I hope now it will run well without issues?

Thank you once again to both of you for such quick response!

Best,
Shweta

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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 :slight_smile: