I am working with the public instance of galaxy and as for the organism I am working with (C. albicans) the genome is not available here, I have to upload a custom reference.
Now I would like to do some RNAseq analysis. I already tried mapping with HISAT2 on one of my samples and also was able to obtain my counts with featureCounts. On the first view this seems to work fine for me. I am also 100% sure, that my feature file is based on the same assembly (and version) that I am using as reference.
But now I read, that one should index the reference genome and that some programs need indexed references? As far as I’ve read, indexing in galaxy is only possible with admin rights (on a local instance), is that correct?
Therefore, I had the idea to upload indexed files of my reference and use them for my mapping with HISAT2. But this did not seem to be possible, as the format of my indexed files seems not to be supported (It is a set of 8 .ht2 files and galaxy recognized them as binary).
Hence, I would like to know, if indexing my reference is really that necessary for the outcome of my data analysis, as it seems to work without indexing as well…? Or is there any possibility to use uploaded indexed genome files? Maybe by changing the format of the files?
And what about programs I would need for wgbs data analysis? First trials here also seemed to work without indexing of my reference.
And could you also explain what indexing does with my reference and which problems could occur, if I do not use an indexed reference?
Thanks for any help!