Hello,
I’m new to using galaxy and RNAseq analysis in general. I wanted to perform reference based RNA-seq analysis oin galaxy n fastq raw read files for Pseudomonas aeruginosa, PA14. I was going through a tutorial to this and reached the mapping step using HISAT2. However, the reference genome file is unavailable in galaxy nor the UCSC bacterial genome database. Is there any way I could obtain the annotated genome fasta for the bacterium in question. Sorry if its a dumb question but I’m fish out of water in these areas. Thank you.
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written
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Gracious •
1 answer
Galaxy related questions are generally best posted in their help forum: https://help.galaxyproject.org/
That said you can download the genome sequence for Pseudomonas aeruginosa, PA14 from NCBI here: https://www.ncbi.nlm.nih.gov/data-hub/genome/GCF_000404265.1/
Use the download button to get both the genome sequence and annotation file. Then upload both to galaxy for use.
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