Question: Question about Galaxy sequence analysis: EBI SRA, NCBI, and dbGap
0
gravatar for snazari1
10 weeks 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 • 129 views
ADD COMMENTlink modified 10 weeks ago by Jennifer Hillman Jackson23k • written 10 weeks ago by snazari10
1
gravatar for Jennifer Hillman Jackson
10 weeks ago by
United States
Jennifer Hillman Jackson23k 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 10 weeks ago • written 10 weeks ago by Jennifer Hillman Jackson23k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 72 users visited in the last hour