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
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