Re: [galaxy-dev] divide fq into 2
On Tue, Mar 08, 2011 at 11:15:44PM -0500, Musa A. Hassan wrote: > Yes I can't get the file into galaxy at all. Am uploading from a file > path. the file is 35mb. When you say "uploading from a filepath" are you using the administrator-only functionality explained here: https://bitbucket.org/galaxy/galaxy-central/wiki/DataLibraries/UploadingFiles _not_ the 'Get Data' -> 'Upload File' selection from the 'Tools' menu? People work with files _much_ larger than that in Galaxy all the time. > Musa > > From: Ry4an Brase [ry4an+gal...@msi.umn.edu] > Sent: Tuesday, March 08, 2011 11:06 PM > To: Musa A. Hassan > Subject: Re: [galaxy-dev] divide fq into 2 > > On Tue, Mar 08, 2011 at 10:44:51PM -0500, Musa A. Hassan wrote: > > Hi Ry4an, > > > > I'd like to do this in galaxy, but the problem is it wont load into > > galaxy. As for using split, the file generated from this returns a > > length mismatch in say Tophat, maybe in the process of splitting the > > file some changes happen to the format. > > So you can't get the file into galaxy at all? Are you trying to upload > it through your browser (suitable only for non-huge files) or are you > using 'upload from file path'? How big (bytes) is the file. > > Also, you should try to keep your replies on the mailing list so that > other searching in the future find the same help. > > -- > Ry4an Brase 612-626-6575 > Software Developer Application Development > University of Minnesota Supercomputing Institutehttp://www.msi.umn.edu -- Ry4an Brase 612-626-6575 Software Developer Application Development University of Minnesota Supercomputing Institutehttp://www.msi.umn.edu ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] divide fq into 2
Yes I can't get the file into galaxy at all. Am uploading from a file path. the file is 35mb. Musa From: Ry4an Brase [ry4an+gal...@msi.umn.edu] Sent: Tuesday, March 08, 2011 11:06 PM To: Musa A. Hassan Subject: Re: [galaxy-dev] divide fq into 2 On Tue, Mar 08, 2011 at 10:44:51PM -0500, Musa A. Hassan wrote: > Hi Ry4an, > > I'd like to do this in galaxy, but the problem is it wont load into > galaxy. As for using split, the file generated from this returns a > length mismatch in say Tophat, maybe in the process of splitting the > file some changes happen to the format. So you can't get the file into galaxy at all? Are you trying to upload it through your browser (suitable only for non-huge files) or are you using 'upload from file path'? How big (bytes) is the file. Also, you should try to keep your replies on the mailing list so that other searching in the future find the same help. -- Ry4an Brase 612-626-6575 Software Developer Application Development University of Minnesota Supercomputing Institutehttp://www.msi.umn.edu ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] divide fq into 2
On Tue, Mar 08, 2011 at 03:43:20PM -0500, Musa A. Hassan wrote: > Hi All, > Is there anyone out there who know how I can divide an fq file containing > illumina short reads randomly into 2 small files contaning approximately > equal number of reads? I have a huge fq from the illumina high-seq platform, > unfortunately, this file is huge and is causing all sorts of problems and I'd > like to divide into to equal sizes(based on number of reads). I'm assuming you mean "in galaxy", right? If so, check out the entries in 'Text Manipulation'. Using 'select first' and 'select last' you can turn one dataset into two datasets each half the size. If instead you mean on the Unix command line, use the tool 'split' or 'head' and 'tail'. -- Ry4an Brase 612-626-6575 Software Developer Application Development University of Minnesota Supercomputing Institutehttp://www.msi.umn.edu ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] divide fq into 2
Hi All, Is there anyone out there who know how I can divide an fq file containing illumina short reads randomly into 2 small files contaning approximately equal number of reads? I have a huge fq from the illumina high-seq platform, unfortunately, this file is huge and is causing all sorts of problems and I'd like to divide into to equal sizes(based on number of reads). Musa ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
