Can someone in Galaxy add the genome for Rickettsia rickettsii to the dropdown list for HISAT2for the reads to

Hi @Sonenshine Thanks for explaining! You need to generate counts for both DESeq2 and Limma, and the same counts files can be used with both, so you only need to do that once. The counts should be against the same reference genome and use the same reference annotation for all of your samples. Wh…

Hi @Sonenshine You can map to any reference genome that you want to within Galaxy. You can also create a custom database key to assign to datasets! FAQ covered in this prior topic. [image] Custom genome + custom build: How to use a genome that is not natively indexed at the server you are worki…

Hi Jennifer: I tried all of the tools you suggested. The custom genome build linked to UCSC. All I could find there were eurkaryote genomes, Archea but NO prokaryotes. I could not find a tool called Custom Reference Genome. The Reference Genome I am trying to install is: Rickettsia rickettsii SSR…

Hi @Sonenshine I’ll try explaining again, let’s start with this part: [image] Sonenshine: I tried all of the tools you suggested. The custom genome build linked to UCSC. All I could find there were eurkaryote genomes, Archea but NO prokaryotes. UCSC will not host every genome. Other common …

Hi Jennifer: Thanks so much for taking the time and finding all these links for me. Most grateful! I have begun uploading the files as per your recommendation. The next step will be to see if HISAT2 will recognize the files and accept them as the reference genome. If there are annotation problems,…

Hi Jennifer: Success, in part. I got HISAT2 to work, followed by Multiqc. Results showed 64% mapping between the two genomes, which is pretty much what I expected since there is considerable biological difference between them (even though they are members of the same genus). The next step, feather…

Hi @Sonenshine Do you mean the tool featureCounts? As far as I know, you can use that tool when counting up any genome’s annotation data versus hits. The other tool you mention, gffread, is for reformatting or parsing reference annotation. If you prepared your annotation already when loading up th…

Hi Jennifer: I got featureCounts to work and I was able to progress through the entire tutorial, ending up mapped counts. Next, I wanted to do a volcano plot and heat map, but the second tutorial, counts to genes, is optimized for mouse and would not work with the bacteria I uploaded. The annodata …

Hi @Sonenshine Limma also works with any genome. XRef: Bioconductor Forum (query=limma) However, AnnotateMyIDs is different. This tool maps from standardized gene identifiers over to public data. You can map other gene identifiers over to ENSEMBL, or use an ENSEMBL based annotation from the sta…

Hi Jennifer: Thanks a bunch. You have provided many options for me to try. Another option would the last step in the tool reads to counts (under transcriptomics). As I recall, it had 3 columns with the last one the counts. Your opinion? Thanks again. Daniel

Hi @Sonenshine I’m not sure I understand … could you explain a bit more about this? I know the step just not what your question is about it. Thanks!

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I am using HISAT2, but my reference genome Rickettsia rickettsii is missing in the dropdown list.