7 days ago by
Galaxy can create
sra data, and it can be stored within Galaxy, but few if any tools use the data directly. And none of those are installed at https://usegalaxy.org or https://usegalaxy.eu. This format is used to submit data to the public repositories. Example: to create an archive: NGS: Mothur > Make.sra creates the necessary files for a NCBI submission.
For analysis in Galaxy, obtain the
fastqsanger version of the data and use that with tools. These can be retrieved using the tools Get Data > ENA SRA and/or NCBI SRA Tools > Download and Extract Reads in FASTA/Q format from NCBI SRA. FAQs: https://galaxyproject.org/support/#basics > Loading Data. With more help about tool inputs and datatypes the groups https://galaxyproject.org/support/#datasets-and-histories && https://galaxyproject.org/support/#getting-inputs-right
There are updated methods for RNA-seq analysis you might want to consider. Please see the Galaxy tutorials here for examples: https://galaxyproject.org/learn/
Note: This question is the followup from this post's comment https://biostar.usegalaxy.org/p/28395/#28397
Next time, please reply back in the same post, it helps keep the conversation thread intact.
Thanks! Jen, Galaxy team