First time user - Genome comparison


Not being a bioinformatician by trade, I was directed to the GalaxyProject as a suitable one-stop-shop for genomic analysis. The project I was trying to achieve was, in principle, quite simple: I have genomic data from two Escherichia coli colonies (a control and an organism that was mutated) and I need to link the phenotypical differences observed to (hopefully sensible) genomic changes that the mutagenesis has introduced.

Unfortunately, the Galaxy software does not seem to want to cooperate. Attempts to use BowTie2 from .fasta files leads to a timeout error; using make.fastq (with the fasta and qvl files), followed by fastqtosam and then bamcompare fails also with “Does not contain mapped reads”).

I am now feeling a bit of decision paralysis: the options seem to numerous, I am not confident there isn’t some issue with my files (I have attached as an example a fasta and qvl file in the hopes someone much more experienced can have a quick perusal and have an eureka moment), and I am hoping the community will be kind enough to gently guide my efforts.

Thanks in advance

Hi @PCDinis

All of this seems to be related to the file contents, and possibly the formats.

If I am understanding your goals correctly, the tutorials here should help.

Each has example data that you can use for file content/format comparisons, then example tool usage, and finally a workflow that you can import and use as a template.

Thank you so much; I shall check the tutorials thoroughly.

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