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Should I "use raw junction" and "Only look for supplied junctions"
by Du, Jianguang 29 Aug '12

29 Aug '12

Dear All, I have two more questions about settings for Tophat. My aim is to look for the defferential splicing events between cell types. After I checked "Use Own Junctions", three more options came out: 1) "Use Gene Annotation Model" 2) "Use raw Junctions" 3) "Only look for supplied junctions" As instructed by Jen, I checked "Use Gene Annotation Model", and input iGenome mm9 genes.gtf as "Gene Model Annotations". However, I am not sure if I should choose to "Use raw junctions" and "only look for supplied junctions". Please help me set up these two options. Thanks. Jianguang

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Installing galaxy with Apache ...
by Neil.Burdett＠csiro.au 28 Aug '12

28 Aug '12

Hi I've installed galaxy with the default settings and it works fine. On a new Ubuntu machine I am trying to get galaxy running with Apache. But I am having problems, I've followed the documentation. After installing Apache I can put my ip address into a browser and I get message saying Apache is working fine. It displays a message from /var/www/index.html Now when I start galaxy I was assuming I would get redirected to the galaxy welcome page, but this doesn't happen and it remains at /var/www/index.html. To view the welcome page I have to add ":8080" after the ip address. Is this still required? I thought that Apache would know to redirect to my distribution....What am I doing wrong? /etc/apache2/sites-available/default-ssl and /etc/apache2/sites-available/default look like this ... DocumentRoot /var/www <Directory /> Options FollowSymLinks AllowOverride None </Directory> <Directory /var/www/> Options Indexes FollowSymLinks MultiViews AllowOverride None Order allow,deny allow from all </Directory> etc ... /var/www/.htaccess RewriteEngine on RewriteRule ^/galaxy$ /galaxy/ [R] RewriteRule ^/galaxy/static/style/(.*) /home/galaxy/galaxy-dist/static/june_2007_style/blue/$1 [L] RewriteRule ^/galaxy/static/scripts/(.*) /home/galaxy/galaxy-dist/static/scripts/packed/$1 [L] RewriteRule ^/galaxy/static/(.*) /home/galaxy/galaxy-dist/static/$1 [L] RewriteRule ^/galaxy/favicon.ico /home/galaxy/galaxy-dist/static/favicon.ico [L] RewriteRule ^/galaxy/robots.txt /home/galaxy/galaxy-dist/static/robots.txt [L] RewriteRule ^/galaxy(.*) http://localhost:8080$1 [P] I created an empty 'galaxy' directory with 777 permissions on it under /var/www and universe_wsgi.ini # Define the proxy-prefix filter. [filter:proxy-prefix] use = egg:PasteDeploy#prefix prefix = /galaxy # ---- Galaxy --------------------------------------------------------------- # Configuration of the Galaxy application. [app:main] filter-with = proxy-prefix cookie_path = /galaxy Thanks Neil

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How to decide if the deference is significant
by Du, Jianguang 28 Aug '12

28 Aug '12

Dear All, I am looking for the deferential splicing events between cell types. I have run the Cuffdiff and I am going through the output file "splicing differential expression testing". I have read the documentation and protocols about how Cuffdiff test for differential expression and regulation. However although I know the changes in relative abundance are quantified by the square root of the Jensen-Shannon divergence, I still could not understand the concept of it (unfortunately I am not good at math and statistics). Is there any way to convert "the square root of the Jensen-Shannon divergence" into "fold of diference"? How much of "the square root of the Jensen-Shannon divergence" equals to 2 fold of difference? Thanks. Jianguang

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Is there web-based CummeRbund?
by Du, Jianguang 28 Aug '12

28 Aug '12

Dear All, I am going to visualize Cuffdiff outputs. I understand that CummeRbund can be used to visualize Cuffdiff outputs. However, I am not good at Linux system and feel difficult to understand CummeRbund manual. Is there web-based CummeRbund program (like Tophat and Cufflink) available for use? If web-based CummeRbund does not exist, is there other web-based program can be used to visualize Cuffdiff outputs? Thanks. Jianguang

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Text Manipulation
by Jennifer Jackson 28 Aug '12

28 Aug '12

Post to mailing list On 8/26/12 11:38 AM, LeeMSilver(a)genepeeks.com wrote: > Hi Jen, > > The ability to use Python commands with the Compute tool seems to be a very well-hidden gem in Galaxy. The problem with this nearly unmentioned gem is the sheer frustration felt when something that works on the Python command line fails on the Galaxy Compute tool. > > What I would like to do is manipulate a column from a UCSC download that lists two or three codons separated by a comma, e.g. AAC,GCG, or GGT, CAC, TAT, . The string-based split command < c5.split(",").pop(1) > fails on this data because Galaxy assigned it a <list> type automatically. All of my attempts to change the data type to "string" have failed. > > Any suggestions? > > Lee > LeeMSilver(a)genepeeks.com -- Jennifer Jackson http://galaxyproject.org

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Please help with the settings for Cufflink, Cuffmerge and Cuffdiff
by Du, Jianguang 28 Aug '12

28 Aug '12

Dear All, I am looking for the differential splicing events between cell types. Although I got a lot of helps from Jen and from protocols found online, I am still not sure about some settings for Cufflink, Cuffmerge and Cuffdiff. 1) For Cufflink: There is a setting for Bias Correction. I made the setting as below: Perform Bias Correction: Yes Reference sequence data: Locally cached Did I make the right settings? 2) For Cuffmerge: As for whether use sequence data, I made the setting as below: Use Sequence Data: Yes Choose the source for the reference list: Locally cached Did I make the right settings? 3) For Cuffdiff: There is another choice whether perform Bias Correction, I made the setting as below: Perform Bias Correction: Yes Reference sequence data: Locally cached Did I make the right settings? Thanks. Jianguang

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Galaxy-France -- Communauté française de Galaxy (French Galaxy Community)
by Dave Clements 27 Aug '12

27 Aug '12

Bonjour à tous, Avec l'aide et le soutien de l'équipe Galaxy, nous venons de mettre en ligne la liste de diffusion Galaxy France. Cette liste a pour but de partager et communiquer sur nos différentes expériences avec Galaxy au sein de l'hexagone. La langue officielle de cette liste est le français. Vous avez besoin d'aide dans l'utilisation de Galaxy, Vous hébergez un serveur public Galaxy, Vous maintenez une instance locale de Galaxy, Vous venez de déposer un outil sur le toolshed, Vous avez des trucs et astuces pouvant interresser la communauté, Vous organisez des formations avec Galaxy, Rejoignez nous en vous inscrivant à http://lists.bx.psu.edu/listinfo/galaxy-france Les archives de cette liste sont disponibles à http://france.list.galaxyproject.org A très bientôt sur la liste Galaxy France, Les administrateurs: Alban Lermine, Olivier Inizan, Rémi Marenco, Dave Clements & Jennifer Jackson ------------------------------ --------------------- Hi everyone, With the help and the support of the Galaxy team, we just put online the Galaxy French mailing list. The aim of this list is to share and communicate on our different experiences with Galaxy in France. * The main language is French. * Topics include, but are not limited to: You need help in the use of Galaxy, You're hosting a Galaxy public server, You're maintaining a local instance of Galaxy, You just add a new tool on the toolshed, You have some tips that could interested the community, You organize workshops with Galaxy, Join us by subscribing at http://lists.bx.psu.edu/listinfo/galaxy-france The list's archives are also available at http://france.list.galaxyproject.org See you soon on the Galaxy-France list, The administrators: Alban Lermine, Olivier Inizan, Rémi Marenco, Dave Clements & Jennifer Jackson -- <http://galaxyproject.org/wiki/GCC2012>http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/

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Please help me check the quality of the Tophat mapping to reference genome
by Du, Jianguang 27 Aug '12

27 Aug '12

Dear All, I ran "Flagstat" under "NGS: SAM Tools" to check the quality of the Tophat output (the file of accepted hits). I got the diagnosis results as follow: 9471730 + 0 in total (QC-passed reads + QC-failed reads) 0 + 0 duplicates 9471730 + 0 mapped (100.00%:-nan%) 0 + 0 paired in sequencing 0 + 0 read1 0 + 0 read2 0 + 0 properly paired (-nan%:-nan%) 0 + 0 with itself and mate mapped 0 + 0 singletons (-nan%:-nan%) 0 + 0 with mate mapped to a different chr 0 + 0 with mate mapped to a different chr (mapQ>=5) I ran Tophat with settings as shown below: Will you select a reference genome from your history or use a built-in index? Use a built-in index Select a reference genome /galaxy/data/mm9/bowtie_index/mm9 Is this library mate-paired? Single-end TopHat settings to use Full parameter list Library Type FR Unstranded Anchor length (at least 3) 8 Maximum number of mismatches that can appear in the anchor region of spliced alignment 0 The minimum intron length 70 The maximum intron length 500000 Allow indel search Yes Max insertion length. 3 Max deletion length. 3 Maximum number of alignments to be allowed 20 Minimum intron length that may be found during split-segment (default) search 50 Maximum intron length that may be found during split-segment (default) search 500000 Number of mismatches allowed in the initial read mapping 1 Number of mismatches allowed in each segment alignment for reads mapped independently 1 Minimum length of read segments 25 Use Own Junctions Yes Use Gene Annotation Model Yes Gene Model Annotations iGenome version of mm9 genes. GTF Use Raw Junctions No Only look for supplied junctions No Use Closure Search No Use Coverage Search Yes Minimum intron length that may be found during coverage search 50 Maximum intron length that may be found during coverage search 20000 Use Microexon Search No Please help me find out what is wrong with the Tophat. Thanks, Jianguang

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Calling SNP
by Francesco Vitiello 27 Aug '12

27 Aug '12

Hi everyone, I'ha a dataset from a sample in Illumina format. I've already groomed the file and aligned to hg19. How can I call SNPs and remove the most common and generally not dangerous? Thank a lot. Francesco -- --

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Extract Spliced Transcripts from Cuffmerge
by Hanson, Sara J 25 Aug '12

25 Aug '12

Hi All, I have mapped RNA-Seq reads to an unannotated partial genome assembly and assembled them into transcripts using the Tuxedo pipeline. II have used the "Extract Genomic DNA" tool to pull the annotated genes out of the genome assembly, but I would like the spliced transcripts as well. Is there a tool or pipeline that can retrieve the exons individually and concatenate them if they are part of the same gene? Any help on this would be much appreciated. Thanks!

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