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Question: Decompression of sra files and further analysis
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gravatar for h.stotz
5 months ago by
h.stotz • 20
European Union
h.stotz • 20 wrote:

Case: 05508803

Dear Jen,

Thanks that you are trying to help me. How can I uncompress the three sra files I have downloaded?

I want to do Tophat and Cufflinks on the sra files to find out the transcripts that correspond to a specific gene BnaA07g22940D in a published genome. I do use https://usegalaxy.org. Any advice would be welcome.

Best wishes,

Henrik
fastq sra rna-seq fastqsanger srr • 225 views
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modified 5 months ago by Jennifer Hillman Jackson ♦ 25k • written 5 months ago by h.stotz • 20
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gravatar for Jennifer Hillman Jackson
5 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

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
ADD COMMENT • link written 5 months ago by Jennifer Hillman Jackson ♦ 25k
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