Large Local File Of Ngs For Fastaq Groomer

Question: Large Local File Of Ngs For Fastaq Groomer

6.8 years ago by

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: 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

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modified 6.8 years ago by Peter Cock • 1.4k • written 6.8 years ago by Arthur Zheng • 50

6.8 years ago by

Peter Cock • 1.4k

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Peter Cock • 1.4k wrote:

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%2 0Files Peter

ADD COMMENT • link written 6.8 years ago by Peter Cock • 1.4k

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

ADD REPLY • link written 6.8 years ago by Arthur Zheng • 50

You must add library files to your current history via the "Shared Data" menu at the top of the Galaxy window. Peter

ADD REPLY • link written 6.8 years ago by Peter Cock • 1.4k

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 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 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/

ADD REPLY • link written 6.8 years ago by Bossers, Alex • 240

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

ADD REPLY • link written 6.8 years ago by Arthur Zheng • 50

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 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

ADD REPLY • link written 6.8 years ago by Bossers, Alex • 240

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