Question: Decompression of sra files and further analysis
gravatar for h.stotz
5 months ago by
European Union
h.stotz20 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 Any advice would be welcome.

Best wishes,


fastq sra rna-seq fastqsanger srr • 225 views
ADD COMMENTlink modified 5 months ago by Jennifer Hillman Jackson25k • written 5 months ago by h.stotz20
gravatar for Jennifer Hillman Jackson
5 months ago by
United States
Jennifer Hillman Jackson25k wrote:


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 or 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: > Loading Data. With more help about tool inputs and datatypes the groups &&

There are updated methods for RNA-seq analysis you might want to consider. Please see the Galaxy tutorials here for examples:

Note: This question is the followup from this post's comment

Next time, please reply back in the same post, it helps keep the conversation thread intact.

Thanks! Jen, Galaxy team

ADD COMMENTlink written 5 months ago by Jennifer Hillman Jackson25k
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