Please find attached this link to my galaxy history. I was stuck trying to complete the walkthrough using this dataset.
Hi Newhe,
Thank you for sharing your history! To best help you, please clarify what problem specifically you are having. Here is what I can gather from your history:
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From your history I see you have imported SRR27333319 which is a paired-end dataset with forward and reverse files.
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I see that you were unable to run kraken2 on your data. Here is how you can do it
a) You can run it on paired reads like so:
b) There is another way to import SRA/SRR files by going to Tools → Get data → Download and Extract Reads in FASTQ tool. This way you get fewer empty files back. You can run Kraken2 the same way as above, in a paired-end manner:
c) This is probably the best way to do it - to treat your files as a collection and to run kraken2 on a collection, because your forward and reverse reads are in a collection - 2 different files appear under a single history element. This way you avoid any ‘hidden’ language. Here is the snapshot:
Please don’t hesitate to reach out for further clarification or questions.