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• Unzip files on Galaxy
    Hello, I have a fastq.gz file downloaded from SRA that need unzipped. How can I do this on Ga...
• No Galaxy Links in EBI SRA - Now what?
  I am trying to import SRA data (SRR1725164) to Galaxy using the Get Data > EBI SRA tool.  Howe...
• Decompression of sra files and further analysis
  Case: 05508803 Dear Jen, Thanks that you are trying to help me. How can I uncompress the thre...
• tophat sra rna seq
  i have sra files from ncbi sra tools i have in my galaxy history. on using tophat i am unable to ...
• converting .sra file to fastq file
  Is there anyway to integrate SRA toolkit into Galaxy? I am trying to analyze raw sra files from G...
• Failure to download data from EBI-SRA to a local Galaxy instance
  Hi, I find that the galaxy downloading link from EBI-SRA doesn't work on my local galaxy instance...
• FIle transfer from GEO to usegalaxy.org
  I'm trying to import some public GEO data into usegalaxy.org - specifically, the mouse RNA-seq da...
• How do you load GEO data into Galaxy
  how do i load files from GEO? these are compressed files of either SRA or TAR files.
• sra data from ncbi
  hi on clicking the link get data- ebi sra i am directed to the ebi website. after finding my sra ...
• Extracting multiple files with NCBI SRA Tools - BAM Fastq Pileup
  Hello I'm trying to import multiple BAM files from NCBI-SRA. A particular sample has 19 runs, e...
• What is the correct regular expression for replacing inconsistent sequence and quality identifiers?
  Hello, I am trying to analyze RNA-Sequence data. The SRA accession number for the file that I am...
• Help with downloading files from EBI SRA
  I am new to galaxy and have been trying to figure out how to align RNA-seq reads to a genome in o...
• SRA conversion program
  How do I convert an SRA file to a fastq or fasta formatted file? I do not see that option in the...
• Does Galaxy Have A Tool For Converting .Sra Files To Fastq Files?
  Hello, I would like to download some GEO files that complement my own research with zebrafish em...
• How to use and program Galaxy to download 300 SRA files at once form the NIH database?
  How to use and program Galaxy to download 300 SRA files at once form the NIH database? We need to...
• Unable to view data of converted srr file into sra format
  Good afternoon, I downloaded an RNAseq file in .srr format using ftp in Galaxy. The file was con...
• How do I process multiple pileup files at once with Varscan to get the vcf files?
  I have a list of 100 SRA IDs for which I need to get the VCF files using VARSCAN. VARSCAN takes...
• Extract reads in FASTQ/A format from NCBI SRA
  Hi. I downloaded an SRA accession. In the results, the spots were separated but is in the same fi...
• SRA files could not retrieved from EBI SRA
  Dear Galaxy Team, There seems to be a persistent problem with importing fastq files from EBI SRA...
• Difference between Fastq and Fastqsanger?
  Hi,  Can somebody briefly explain the difference between fastq and fastqsanger files in Galaxy? ...
• How to check unaligned reads?
  I have a pair end SRA files for which I have done FASTQc. The SRA files are then mapped against ...
• BAM dataset plain text view within Galaxy
  Viewing Alignment of mRNAseq SRAs to an uploaded cDNA reference genome I uploaded an SRA accessi...