Dear Jen Thanks. I have merged the files and end up with 4 x 47 G fastq files for read mapping to the reference. It seems this is too much data to analyse on the public main instance if the size limit is 250 G? So I tried to set up the cloud option following the screencast (http://screencast.g2.bx.psu.edu/cloud/), but when I search for the current AMI name (861460482541/galaxy-cloudman-2011-03-22) it is not found in the list of community AMIs under Amazon's EC2 Management Console. Any ideas why this is not working? regards Andrew
________________________________ From: Jennifer Jackson [j...@bx.psu.edu] Sent: 08 April 2013 21:21 To: Thompson, Andrew Cc: 'galaxy-user@lists.bx.psu.edu' Subject: Re: [galaxy-user] merging fastq files Hi Andrew, Merging the data prior to upload would probably be simplest. Files in a galaxy history are not in .tar format at this time. Loading forward and reverse separately will most likely be important from a scientific perspective for analysis. Once ready for upload, you can tar or gz - as long as each load is a single file - or leave uncompressed - either is fine. Using FTP is required for larger data (>= 2G) and using a client that will allow you to track progress/resume an interrupted load can be helpful. Each file can be up to 50G in size if you have an account. http://wiki.galaxyproject.org/FTPUpload Hopefully this helps, Jen Galaxy team On 4/5/13 3:20 AM, Thompson, Andrew wrote: Hi I have received Illumina paired-end genome sequence data as a .tar file. When unpacked the data for each genome accession is split into about 100 fastq files. Total of about 37 Gpb per genome. Can you recommend the best way to organise this data prior to mapping to reference genome? I can concatenate unpacked files using DOS command line into forward and reverse before uploading: is this the best approach? Is there a tools that will start with the .tar file? Andrew ___________________________________________________________ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
