[galaxy-user] What is the quality score type for the Solid datasets downloaded from SRA of NCBI?
Hi all, Please help with the quality score type for the downloaded Solid datasets. I downloaded RNA-seq datasets, which were generated by AB Solid system, as base space and at FastQ format from SRA of NCBI. I uploaded the datasets onto the online sever Galaxy and change the datatype directly into fastqsanger and then test the quality by running FastQC. The output per base quality of solid dataset (please take look at the attached figure per_base_quality-Solid) is quite different from the output per base quality of Illumina dataset (please compare with the attached figure per base quality-Illumina). The top score for Solid dataset is about 31, however the top score for Illumina dataset is 38. What is the quality score type for the downloaded Solid datasets when downloaded as base space and at FastQ format from SRA of NCBI? Please help me solve this problem. Thanks. Best regards. Jianguang Du attachment: per_base_quality-Illumina.pngattachment: per_base_quality-Solid.png___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] What is the quality score type for the Solid datasets downloaded from SRA of NCBI?
Hello Jianguang, The tool NGS: QC and manipulation - FASTQ Groomer has some information about this, including a link to a wikipedia entry with more details specifically about the SRA: http://en.wikipedia.org/wiki/FASTQ_format http://en.wikipedia.org/wiki/FASTQ_format#NCBI_Sequence_Read_Archive And here is the SRA submission form, although the experimental record you downloaded from is the best place to find details: https://www.ebi.ac.uk/ena/about/sra_data_format SRA accepts CS and Fastq. In Galaxy these translate to: Color space reads: - datatype Color Space Sanger - annotated as fastqcssanger Fastq reads: - datatype with Phred quality offset 64 Illumina 1.3-1.7 - annotated as fastqillumina and - datatype with Phred quality offset 33 Illumina 1.8+ - annotated as fastqsanger Many tools require fastqsanger. Use the FASTQ Groomer to transform as needed, but double check with FastQC just like you are doing. I have seen data labeled as Illumina 1.5 that was really already scaled to Phred+33, or at least appeared to be. In the end this is a judgement call or you can try to contact SRA/data authors for a definitive answer if there are no processing notes in the experiment (often the case). Hopefully this helps, Jen Galaxy team On 3/5/13 8:18 AM, Gene Genome wrote: Hi all, Please help with the quality score type for the downloaded Solid datasets. I downloaded RNA-seq datasets, which were generated by AB Solid system, as base space and at FastQ format from SRA of NCBI. I uploaded the datasets onto the online sever Galaxy and change the datatype directly into fastqsanger and then test the quality by running FastQC. The output per base quality of solid dataset (please take look at the attached figure per_base_quality-Solid) is quite different from the output per base quality of Illumina dataset (please compare with the attached figure per base quality-Illumina). The top score for Solid dataset is about 31, however the top score for Illumina dataset is 38. What is the quality score type for the downloaded Solid datasets when downloaded as base space and at FastQ format from SRA of NCBI? Please help me solve this problem. Thanks. Best regards. Jianguang Du ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] Local galaxy install vs cloudman
Hello, The cloud version of Galaxy is quite easy to fire up and is very complete with all tools and genomes preinstalled. Local installation on the other hand is painful, contrary to the nice descriptions among the wiki pages. For exmples, see this: http://vallandingham.me/installing_galaxy_tools.html The initial install of galaxy is easy enough, but making a complete setup is quite painful without dedicated IT people. Setting up ftp server access for uploading and installing tool dependencies in particular are not pleasant. Since the cloud version comes with everything including the kitchen sink, would it be possible to create a more compete local install bundle that also includes everything, without resorting to running a VM locally? Have I missed some other really easy process? Thanks, Jim ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Local galaxy install vs cloudman
H Jim, The components for the cloud version are built in an automated fashion using CloudBioLinux scripts (https://github.com/chapmanb/cloudbiolinux) so maybe using those can get you closer to what you're after? Cheers, Enis On Wed, Mar 6, 2013 at 5:17 AM, James Vincent j...@uvm.edu wrote: Hello, The cloud version of Galaxy is quite easy to fire up and is very complete with all tools and genomes preinstalled. Local installation on the other hand is painful, contrary to the nice descriptions among the wiki pages. For exmples, see this: http://vallandingham.me/installing_galaxy_tools.html The initial install of galaxy is easy enough, but making a complete setup is quite painful without dedicated IT people. Setting up ftp server access for uploading and installing tool dependencies in particular are not pleasant. Since the cloud version comes with everything including the kitchen sink, would it be possible to create a more compete local install bundle that also includes everything, without resorting to running a VM locally? Have I missed some other really easy process? Thanks, Jim ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
