Large local file of NGS for FASTAQ Groomer
Hi, I have downloaded and installed a local instance of galaxy on the linux server using my user account according to here: http://main.g2.bx.psu.edu/ Then I ran the following command:
sh run.sh and accessed galaxy through the local firefox browser on the server http://localhost:8080
Now I am trying to use some NGS files for FASTQ Groomer. Each file is in the server disk already, but very large (~8G each). I was not able to use the "upload file from your computer" function under the "Get Data" tab (maybe because each file is too large). What am I supposed to do? Thank you! Arthur
On Sun, Feb 12, 2012 at 10:28 PM, Arthur Zheng <haoz021@gmail.com> wrote:
Hi,
I have downloaded and installed a local instance of galaxy on the linux server using my user account according to here: http://main.g2.bx.psu.edu/
Then I ran the following command:
sh run.sh and accessed galaxy through the local firefox browser on the server http://localhost:8080
Now I am trying to use some NGS files for FASTQ Groomer. Each file is in the server disk already, but very large (~8G each). I was not able to use the "upload file from your computer" function under the "Get Data" tab (maybe because each file is too large).
What am I supposed to do?
Thank you!
Arthur
The method you tried "uploads" the file from your computer back to itself - making a copy as it goes with lots of overhead. You should probably consider the procedure here which allows you to avoid even making a copy on disk but point at the existing files already on the server: http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files Peter
On Sun, Feb 12, 2012 at 4:34 PM, Peter Cock <p.j.a.cock@googlemail.com>wrote:
Hi,
I have downloaded and installed a local instance of galaxy on the linux server using my user account according to here: http://main.g2.bx.psu.edu/
Then I ran the following command:
sh run.sh and accessed galaxy through the local firefox browser on the server http://localhost:8080
Now I am trying to use some NGS files for FASTQ Groomer. Each file is in
On Sun, Feb 12, 2012 at 10:28 PM, Arthur Zheng <haoz021@gmail.com> wrote: the
server disk already, but very large (~8G each). I was not able to use the "upload file from your computer" function under the "Get Data" tab (maybe because each file is too large).
What am I supposed to do?
Thank you!
Arthur
The method you tried "uploads" the file from your computer back to itself - making a copy as it goes with lots of overhead. You should probably consider the procedure here which allows you to avoid even making a copy on disk but point at the existing files already on the server:
http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files
Peter
Hi Peter, I have followed the link you provided and selected the option "Upload directory of files". Now my NGS data are in the library, and I am wondering how I can feed them to FASTQ Groomer? Thanks! Arthur
On Mon, Feb 13, 2012 at 2:17 AM, Arthur Zheng <haoz021@gmail.com> wrote:
On Sun, Feb 12, 2012 at 4:34 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Sun, Feb 12, 2012 at 10:28 PM, Arthur Zheng <haoz021@gmail.com> wrote:
Hi,
I have downloaded and installed a local instance of galaxy on the linux server using my user account according to here: http://main.g2.bx.psu.edu/
Then I ran the following command:
sh run.sh and accessed galaxy through the local firefox browser on the server http://localhost:8080
Now I am trying to use some NGS files for FASTQ Groomer. Each file is in the server disk already, but very large (~8G each). I was not able to use the "upload file from your computer" function under the "Get Data" tab (maybe because each file is too large).
What am I supposed to do?
Thank you!
Arthur
The method you tried "uploads" the file from your computer back to itself - making a copy as it goes with lots of overhead. You should probably consider the procedure here which allows you to avoid even making a copy on disk but point at the existing files already on the server:
http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files
Peter
Hi Peter,
I have followed the link you provided and selected the option "Upload directory of files". Now my NGS data are in the library, and I am wondering how I can feed them to FASTQ Groomer?
Thanks!
Arthur
You must add library files to your current history via the "Shared Data" menu at the top of the Galaxy window. Peter
Are you sure the fastq's are in older format? Otherwise you won't need to groom the files anymore (as far as I understood) since the newer format is comparable Sanger quality score already.... Saves huge resources! Alex -----Oorspronkelijk bericht----- Van: galaxy-user-bounces@lists.bx.psu.edu [mailto:galaxy-user-bounces@lists.bx.psu.edu] Namens Peter Cock Verzonden: maandag 13 februari 2012 11:04 Aan: Arthur Zheng CC: galaxy-user@lists.bx.psu.edu Onderwerp: Re: [galaxy-user] Large local file of NGS for FASTAQ Groomer On Mon, Feb 13, 2012 at 2:17 AM, Arthur Zheng <haoz021@gmail.com> wrote:
On Sun, Feb 12, 2012 at 4:34 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Sun, Feb 12, 2012 at 10:28 PM, Arthur Zheng <haoz021@gmail.com> wrote:
Hi,
I have downloaded and installed a local instance of galaxy on the linux server using my user account according to here: http://main.g2.bx.psu.edu/
Then I ran the following command:
sh run.sh and accessed galaxy through the local firefox browser on the server http://localhost:8080
Now I am trying to use some NGS files for FASTQ Groomer. Each file is in the server disk already, but very large (~8G each). I was not able to use the "upload file from your computer" function under the "Get Data" tab (maybe because each file is too large).
What am I supposed to do?
Thank you!
Arthur
The method you tried "uploads" the file from your computer back to itself - making a copy as it goes with lots of overhead. You should probably consider the procedure here which allows you to avoid even making a copy on disk but point at the existing files already on the server:
http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library% 20Files
Peter
Hi Peter,
I have followed the link you provided and selected the option "Upload directory of files". Now my NGS data are in the library, and I am wondering how I can feed them to FASTQ Groomer?
Thanks!
Arthur
You must add library files to your current history via the "Shared Data" menu at the top of the Galaxy window. Peter ___________________________________________________________ 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/
Dear Alex, Thank you for the reminder. I noticed that I am using illumina CASAVA 1.8. How can I make sure whether it is already in Sanger format or not? Arthur On Mon, Feb 13, 2012 at 4:53 AM, Bossers, Alex <Alex.Bossers@wur.nl> wrote:
Are you sure the fastq's are in older format? Otherwise you won't need to groom the files anymore (as far as I understood) since the newer format is comparable Sanger quality score already.... Saves huge resources! Alex
Arthur, When the data is coming from casavA 1.8 (actually I believe from 1.5 and above) I think it's already in the proper format. An excellent overview is here: http://en.wikipedia.org/wiki/FASTQ_format Basically the headers of the fastq reads are my indication at the moment. Since 1.8 it changed to @SOMETHING<space>READINFO. Most current seqlabs deliver that format. Good luck! Alex PS: correct me when wrong about the phred scoring. Probably PeterC knows this best since he wrote the python groomer. Van: Arthur Zheng [mailto:haoz021@gmail.com] Verzonden: dinsdag 14 februari 2012 6:01 Aan: Bossers, Alex CC: galaxy-user@lists.bx.psu.edu Onderwerp: Re: [galaxy-user] Large local file of NGS for FASTAQ Groomer Dear Alex, Thank you for the reminder. I noticed that I am using illumina CASAVA 1.8. How can I make sure whether it is already in Sanger format or not? Arthur On Mon, Feb 13, 2012 at 4:53 AM, Bossers, Alex <Alex.Bossers@wur.nl<mailto:Alex.Bossers@wur.nl>> wrote: Are you sure the fastq's are in older format? Otherwise you won't need to groom the files anymore (as far as I understood) since the newer format is comparable Sanger quality score already.... Saves huge resources! Alex
participants (3)
-
Arthur Zheng -
Bossers, Alex -
Peter Cock