Re: [galaxy-user] Summary Statistics
Hi Dominique, I’d use the original fasta file and input it into the 'Fasta Manipulation Compute Sequence Length' tool Then, using the output, run the 'Statistics Summary Statistics for any numerical column' tool on c2. That will give you all the info you’re after. Cheers, Graham Dr. Graham Etherington Bioinformatics Support Officer, The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH. UK Tel: +44 (0)1603 450601 Twitter: @bioinformatiks From: Dominique Cowart dac...@gmail.commailto:dac...@gmail.com Date: Friday, 23 May 2014 12:29 To: galaxy-u...@bx.psu.edumailto:galaxy-u...@bx.psu.edu galaxy-u...@bx.psu.edumailto:galaxy-u...@bx.psu.edu Subject: [galaxy-user] Summary Statistics Hello, I am attempting to use Galaxy to calculate the mean sequence read length and identify the range of read lengths for my 454 data. The data has already been divided into columns: HD4AU5D01BHBCQCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC HD4AU5D01A093MCTCTGTCGCTCTGTCTCTCTTCTCTCTCTCTCTCTCT I have attempted to use the Summary Statistics button, however it appears to only be for numerical data and not sequence data. Is this tool/task available via Galaxy? Thank you in advance, Dominique Cowart ___ The Galaxy User List is being replaced by the Galaxy Biostar User Support Forum at https://biostar.usegalaxy.org/ Posts to this list will be disabled in May 2014. In the meantime, you are encouraged to post all new questions to Galaxy Biostar. 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/
[galaxy-user] Creating a Trackster visualisation from a reference in your history
Hi, I’m struggling to figure out how to visualise a SAM file in Trackster as a normal user (i.e. without admin privileges). I’ve tried both my local install and use galaxy.org. This is what I’ve done on usegalaxy.org: Uploaded paired-end fastq sequences and a reference fasta file. Mapped with BWA. Clicked on SAM output – Visualize Trackster Chose 'View in new visualisation’, then ‘Add a Custom Build’. In the ‘Add a Custom Build’ I give my build the name ‘solanum_reference’ and the key ‘solanum_reference_1’. I select the fasta mapping reference from my history under the ‘FASTA’ tab and under the Len File entry I upload a .len file (tab-delimited) called ‘solanum_reference_1.len’. I navigate back to my SAM history item, associate the Database/Build with my new build (via the Edit attributes icon) and then again Visualize Trackster View in New Visualization. I name the Browser, select my ‘solanum_reference’ as the 'Reference genome build' and hit ‘Create’. The view changes to the Trackster Browser and at the top I reads: Preparing data, This can take a while for a large dataset…..etc., etc. After a few minutes, this changes too: “Cannot display dataset due to an error.” If I click on ‘View error’ I get: Couldn't open /galaxy/data/chrom/solanum_reference_1.len , No such file or directory Is it possible to create a custom build and use it to view a SAM file without adding the .len and .2bit files in to the Galaxy file system as an administrator? If so, what am I doing wrong? Many thanks, Graham Dr. Graham Etherington Bioinformatics Support Officer, The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH. UK Tel: +44 (0)1603 450601 ___ 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/
Re: [galaxy-user] Cuffdiff version not apparent
Hi Cory, A list of Galaxy dependancies can be found on the wiki at: http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies ...although many tools allow a range of tool versions. You can also identify the information about the specific tool versions by clicking on the View Details Œi¹ icon of a history item created by that tool and looking at the Tool Version field. If you¹re using the Galaxy public server (https://usegalaxy.org/) then clicking on the Œi¹ icon of a cuffdiff output file will show: Tool Version:cuffdiff v2.1.1 (4046M) Hope this helps. Cheers, Graham Dr. Graham Etherington Bioinformatics Support Officer, The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH. UK Tel: +44 (0)1603 450601 On 04/11/2013 20:57, Cory Dunn cd...@ku.edu.tr wrote: Dear Galaxy Staff: I was wondering which version of Cuffdiff is currently running on Galaxy. The wrapper version is 0.0.6, but I did not see the actual version of the underlying software under the Tool Version field (please see attached screen grab). Thanks for your help, Cory Dunn ___ 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/
Re: [galaxy-user] History items remain pending (grey color)
Hi Priya, If you are using one of the public Galaxy servers (e.g. http://main.g2.bx.psu.edu/), then it's quite probable that there a lots of jobs queued in the system by other users. If your history item is grey that means the job has been successfully submitted and is waiting its turn in the queueing system. When the system is busy it will take longer for the jobs to be submitted due to the high demand. In short - give it some time, it will run eventually. Best wishes, Graham Dr. Graham Etherington Bioinformatics Support Officer, The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH. UK Tel: +44 (0)1603 450601 On 25/03/2013 23:01, Priya Bhatt priya.bh...@loni.ucla.edu wrote: Dear Galaxy Users, Forgive me in advance, but I am a VERY new Galaxy user! I am trying to go through the Galaxy 101 tutorial provided on the galaxy website (https://main.g2.bx.psu.edu/u/aun1/p/galaxy101). The first step asks to get exon data of Chromosome 22 from UCSC database, and the second step asks to get the SNP data from the same database. When I do these two steps, I understand the history items should turn green once they are processed, however after a few hours these items remain grey. Am I doing something wrong? Any help would be greatly appreciated! Thank you in advance, Priya ___ 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/ ___ 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/
Re: [galaxy-user] extract genome sequence
Yan, One way to do this is to create an interval file with the new co-ordinates (+/- 5kb) and then use the Fetch Sequences Extract genomic DNA tool. To create a new co-ordinates file, input your annotation file into the Text Manipulation Compute tool, using expressions like c3 = c3-5000 to get your new co-ordinates. You'll get 2 new columns in the final output file and then use the Text Manipulation Cut tool to extract the columns you need to create an interval file. Hope this helps. Cheers, Graham Dr. Graham Etherington Bioinformatics Support Officer, The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH. UK Tel: +44 (0)1603 450601 On 24/09/2012 09:02, Björn Grüning bjoern.gruen...@pharmazie.uni-freiburg.de wrote: Hi Yan, did you know the tool extractfeat from the EMBOSS suite (its in the toolshed)? I don't know offhand if it can work in batch mode, but its possible to add that feature. Cheers, Bjoern Hi everyone, I have the genome sequence and gene annotation file. Is there a tool on Galaxy to extract the 5,000 bp upstream, 5,000 bp downstream and genome sequences of the genes (including exons and introns) from the genome sequence? Any suggestions are highly appreciated! Thanks! Yan ___ 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/ -- Björn Grüning Albert-Ludwigs-Universität Freiburg Institute of Pharmaceutical Sciences Pharmaceutical Bioinformatics Hermann-Herder-Strasse 9 D-79104 Freiburg i. Br. Tel.: +49 761 203-4872 Fax.: +49 761 203-97769 E-Mail: bjoern.gruen...@pharmazie.uni-freiburg.de Web: http://www.pharmaceutical-bioinformatics.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/ ___ 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/
Re: [galaxy-user] Chip-seq data
Giuseppe, Your ChipSeq data is already in fastq format. It appears to have Illunima quality scores, so you'll need to use the NGS:QC and manipulation FASTQ Groomer tool, using 'Illumina 1.3+' as input and 'Sanger' quality format as output. As to using MACS, I've never used it before but you should be able to get your answers by reading the manual at: http://liulab.dfci.harvard.edu/MACS/README.html Hope this helps, Graham Dr. Graham Etherington Bioinformatics Support Officer, The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH. UK Tel: +44 (0)1603 450601 On 29/11/2011 15:16, Giuseppe Petrosino petros...@ceinge.unina.it wrote: Hi,I have illumina ChipSeq data in txt format with this structure: @HWI-EAS225:8:1:1:58#0/1 NAGAGTGCCCGGGTTCAGTTCTCAGCACCCATGTGG +HWI-EAS225:8:1:1:58#0/1 DMSSUSSTTTUTSRQRTTTSSSUS @HWI-EAS225:8:1:1:1803#0/1 NCCATGGGAAGAGCTGGGCAGGCGGGCCGAGCGAAG +HWI-EAS225:8:1:1:1803#0/1 DLSTTSKOUTRRTTSSSSRPNNTOJOTSSRTB @HWI-EAS225:8:1:1:1547#0/1 NAGGGGTGGGACTGGCACTTGCCTCTACCAGC +HWI-EAS225:8:1:1:1547#0/1 DLVVVTPTUVVWVVUVVUWVVVWWWVVV Can I convert into Fastq format?If so, how can I? Furthermore, after using Map with Bowtie for Illumina, how can I use MACS (Model-based Analysis of ChIP-Seq) if I have two files for IP samples and two files for Control samples? Thank you so much. Giuseppe ___ 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/
Re: [galaxy-user] 'Draw quality score Boxplot' error
Caroline, I've had this problem before and find that although the job 'fails', the boxplot is actually created. If you click on the 'eye' in the boxplot history item, you should still be able to see and save your plot. Regards, Graham Dr. Graham Etherington Bioinformatics Support Officer, The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH. UK Tel: +44 (0)1603 450601 On 28/11/2011 16:21, Avik Datta reach4a...@gmail.com wrote: Hi Caroline, Try to change the default font of gnuplot http://www.gnuplot.info/faq/faq.html#SECTION0009 On Thu, Nov 24, 2011 at 3:35 PM, Caroline Proux k...@pasteur.fr wrote: Hi,I have illumina ChipSeq data and I want to use the Draw quality score Boxplot I run thequality format converter (ASCII numeric). But the Draw quality score Boxplot do an error An error occurred running this job:Could not find/open font when opening font arial, .. where is my problem? thank you so much Caroline Proux ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org http://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/ -- Avik Datta ___ 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/
Re: [galaxy-user] Regarding .exe file
Shambhavi, Any tool that can be run from the command line, whether it be a .exe, .sh, .pl, .ph, etc, can be installed in Galaxy. All this is explained on the wiki. The best page to start would be: http://wiki.g2.bx.psu.edu/Admin/Tools Cheers, Graham Dr. Graham Etherington Bioinformatics Support Officer, The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH. UK Tel: +44 (0)1603 450601 On 14/11/2011 04:47, Shambhavi Srivastava shambhavi.srivast...@gmail.com wrote: Dear Galaxy users, Is it possible to install .exe files in galaxy?If yes then how? Thanx, Shambhavi ___ 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/
Re: [galaxy-user] version tophat and cufflinks
Hi Dongdong, The version of TopHat is 1.2.0 and Cufflinks is 1.0.1. The full list of all Galaxy dependencies can be found on the wiki at: http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies All the best, Graham Dr. Graham Etherington Bioinformatics Support Officer, The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH. UK Tel: +44 (0)1603 450601 From: dongdong zhaoweiming zhaoweiming1...@yahoo.com.cnmailto:zhaoweiming1...@yahoo.com.cn Date: Mon, 10 Oct 2011 17:57:51 +0100 To: galaxy-user@lists.bx.psu.edumailto:galaxy-user@lists.bx.psu.edu galaxy-user@lists.bx.psu.edumailto:galaxy-user@lists.bx.psu.edu Subject: [galaxy-user] version tophat and cufflinks Hi, May I ask what is the version of TopHat and cufflinks in the galaxy? Thanks a lot! weimin zhao ___ 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/
[galaxy-user] Manipulate FASTQ question
Hi,
I currently have read names with the format:
@N57638:1:64JU0AAXX:1:1:1057:943 1:Y:0:
and would like to change them to the format:
@N57638:1:64JU0AAXX:1:1:1057:943/1
I use Manipulate FASTQ, on all reads and set 'Manipulate Reads on:' to
'Name/Identifier', ('String Translate' becomes the only option).
I then set the 'From:' field to '1:Y:0:' and the 'To:' field to '/1' (without
the literal quotes).
I get the following error:
Traceback (most recent call last):
File
/home/home/galaxy/software/galaxy-central/tools/fastq/fastq_manipulation.py,
line 37, in
main()
File
/home/home/galaxy/software/galaxy-central/tools/fastq/fastq_manipulation.py,
line 25, in main
new_read = fastq_manipulator.match_and_manipulate_read( fastq_read )
File
/home/home/galaxy/software/galaxy-central/database/job_working_directory/942/tmpgp13Qy,
line 15, in match_and_manipulate_read
new_read = manipulate_read( fastq_read )
File
/home/home/galaxy/software/galaxy-central/database/job_working_directory/942/tmpgp13Qy,
line 8, in manipulate_read
new_read.identifier = @%s % new_read.identifier[1:].translate( maketrans(
binascii.unhexlify( 313a593a303a ), binascii.unhexlify( 2f31 ) ) )
ValueError: maketrans arguments must have same length
So, do the From and To fields really need to be the same length?
This seems rather strange and unhelpful.
Am I doing something wrong?
Many thanks,
Graham
Dr. Graham Etherington
Bioinformatics Support Officer,
The Sainsbury Laboratory,
Norwich Research Park,
Norwich NR4 7UH.
UK
___
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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:
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