February 2011 - galaxy-user - lists.galaxyproject.org

FastX Clipper on FastQ data
by Michael Walter 17 Feb '11

17 Feb '11

Hi List, I have a couple of miRNA-Seq files (Illumina GAIIx, 29nt read length). These reads contain differing amounts of 3' adapter sequences and therefore map really badly to the human genome (with eland v2). Therefore, I'd like to use the FastX clipper tool, which states that "This tool clips adapters from the 3'-end of the sequences in a FASTA/FASTQ file." However, After uploading my fastq files and converting it to Sanger format, the clipper does not accept the fastq file as input. After converting it to fasta it works fine. However, the mapping tools will only accept fastq files. So my question is, is there a way to clip the adapter directly in the fastq file (we have a local installation of galaxy, so I may also use command line options)? Thank you very much for your input, Mike -- Dr. Michael Walter MFT Services University of Tübingen Calwerstr. 7 72076 Tübingen Tel.: +49 7071 29 83210 Fax. + 49 7071 29 5228 web: www.mft-services.de Confidentiality Note: This message is intended only for the use of the named recipient(s) and may contain confidential and/or proprietary information. If you are not the intended recipient, please contact the sender and delete the message. Any unauthorized use of the information contained in this message is prohibited.

3 3

Upload via SCP?
by Felix Hammer 17 Feb '11

17 Feb '11

Hi, is it possible to use SCP to upload files instead of FTP? thxbye, Felix

2 1

Filename extension in new tool
by Sean Davis 17 Feb '11

17 Feb '11

I have a tool that takes a pdb file as input. The authors of the *compiled* code require that the suffix be either ".pdb" or ".ent". When I upload a .pdb file, the filename that gets fed to the tool now ends in .dat. What is the best way to get the original file extension stored in the file database? Thanks, Sean

2 2

Error message saving file from Galaxy
by vasu punj 16 Feb '11

16 Feb '11

I had problem in the past saving sam file from Galaxy's floppy sign and at that time Jen mentioned there was a bug which was fixed. After a month or so I cannot save the file. Any one has any suggestion please error message snapshot attached. I am running Galaxy on local server. Thanks.

1 0

Which tools can a file be used with?
by Geoff Jentry 16 Feb '11

16 Feb '11

I'm starting to poke around wtih Galaxy. Suppose I have a file that I've uploaded, or pulled in by some other mechanism. When I look at a tool that can use that type of file, it'll be auto-filled in on the dropdown for the file input on that tool. As an example, if I upload a FASTA file, I'll see that data file in the "Convert these sequences" dropdown under the FASTA-to-Tabular tool. Is there some way to see a comprehensive list of tools that are enabled for a particular data file? Thanks -J

2 1

Problems using aaChanges tool
by Evan Schwab 16 Feb '11

16 Feb '11

Hi, I am trying to use the aaChanges tool. I have a file of SNPs in the correct interval format and a UCSC uploaded bed file of genomic intervals. These are both for the Zebrafish Zv9 build and are appropriately labeled this way in their attributes. But when I try to run the tool it says for both the SNP interval file and UCSC bed file: "Sequences are not currently available for the specified build." Am I doing something wrong with my formatting or does this tool not yet support Zebrafish Zv9 build? I tried using it in the Human Genome Variation section of the main Galaxy site as well as the Evolution section of the test site and both gave me the same error. Please let me know what is happening. Thank you so much Evan -- Evan Schwab Research Associate Megason Lab Department of Systems Biology Harvard Medical School 200 Longwood Ave Boston, MA 02115 908-938-3779

2 2

Data upload question
by Haiping Hao 16 Feb '11

16 Feb '11

Hi, I am new to Galaxy and trying to upload some data files. The size of my compressed file is about 7 GB, how long it will take to upload one file? Thank you. Haiping -- ---------------------------------------------- JHMI Deep Sequencing and Microarray Core Facility at BRB - Your source for quality service on Microarray studies, NextGen Sequencing, and Data Analysis. http://www.microarray.jhmi.edu/ ---------------------------------------------- Haiping Hao Ph.D. Manager Johns Hopkins University Deep Sequencing and Microarray Core 733 N. Broadway, Rm 359 Baltimore, MD 21205 hhao(a)jhmi.edu Phone: 443-287-9056 Fax: 410-502-6666

3 2

Missing scrollbars on openid page
by Peter 16 Feb '11

16 Feb '11

Hi all, I ran into a small issue with account creation, likely to affect people using a netbook or other device with a low (vertical) resolution. I don't think I have an account on main.g2.bx.psu.edu so I tried using OpenID via GoogleMail. This brought me to the following page: http://main.g2.bx.psu.edu/user/openid_associate?username=&status=warning&me… There are no scroll bars on this page (which usually means the page explicitly disabled them), and it is too long to fit on my screen without zooming out so much that I can hardly read it. I'm using Firefox 3.6 on Linux. (I then got a username clash, and realised I'd already made an account with a different email address) Peter

2 2

Mapping does not start
by Felix Hammer 15 Feb '11

15 Feb '11

Hi, I am trying to map sequences with Bowtie. Have been waiting for a few hours now but it still says "Job is waiting to run". A few days ago I didn't have this problem and the job started immediately. My guess is that the jobs are still stuck in a queue? How can I tell when the jobs will approximately start running? Is there a way to view the queue position? thx, Felix

2 2

data upload problem
by Yanji Xu 15 Feb '11

15 Feb '11

Dear Sir/Madam, I downloaded Galaxy and installed it locally. In my test run, I tried to upload a fastq file, which is about 2.8G. However, the data upload has taken more than 3 days, but still not finished. The error message I found is "OverflowError: signed integer is greater than maximum". Could you please let me know how to resolve this problem and upload my file? Do you have any training classes? Thanks, Yanji

1 0