Question: Question about Galaxy sequence analysis: EBI SRA, NCBI, and dbGap
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gravatar for snazari1
8 months ago by
snazari10
snazari10 wrote:

I am using Galaxy for a class I'm teaching and came across a question...I chose Get data and then EBI SRA and entered in the search box "SRS072363" .According to the text book I am following (exploring Bioinformatics) I should see 2 files of Illumina sequence data in FASTQ format. But instead I see 12 different accession results with no file to download. How can I get around this problem to get my Illumina sequence data in FASTQ format for SR072363. Thank you

fastq sra ebi-sra ncbi dbgap • 312 views
ADD COMMENTlink modified 8 months ago by Jennifer Hillman Jackson25k • written 8 months ago by snazari10
1
gravatar for Jennifer Hillman Jackson
8 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

For this study, the notes at EBI SRA state "Go to dbGap" for the data. Please see: https://www.ncbi.nlm.nih.gov/pubmed/24297256

Use the tool NCBI SRA Tools > Download and Extract Reads in FASTA/Q format from NCBI SRA with each of the SRR accessions listed at EBI SRA to extract the fastq data into Galaxy.

The accession I tested (SRR057872) has interlaced /1 (forward) and /3 (reverse) reads, which means the other data is probably formatted this way too. This is how to de-interlace: https://galaxyproject.org/support/ncbi-sra-fastq/

Be sure to do some QA on the data: https://galaxyproject.org/tutorials/ngs/

Support FAQs: https://galaxyproject.org/support/

Hope that helps! Jen, Galaxy team

ADD COMMENTlink modified 8 months ago • written 8 months ago by Jennifer Hillman Jackson25k
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