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Re: [galaxy-user] Finding constitutive exons using expression data (7plusorminus 3)
by Sébastien Vigneau 10 Feb '14

10 Feb '14

Hi 7plusorminus 3, One possibility is to use the "group" tool with "max" operation, to get the highest expressed exon for each gene. Then, you may use "subtract datasets" to remove the highest expressed exons from the original dataset, and iterate to get the second highest expressed exons (which are now the highest expressed exons). "Group" may also help you getting the exons with more proximal or distal start position (whether it is 5' or 3' depends on the orientation of the gene). Alternatively, if you know how to use R, you can use the function "by" (here is a good explanation: http://nsaunders.wordpress.com/2010/08/20/a-brief-introduction-to-apply-in-… ). Sébastien ---------------------------------------- Message: 1 Date: Sun, 9 Feb 2014 16:43:14 -0500 From: 7plusorminus 3 <7plusorminus3(a)gmail.com> To: galaxy-user(a)lists.bx.psu.edu Subject: [galaxy-user] Finding constitutive exons using expression data Message-ID: <CALfFDirXk1LYY6t+JHnnRCfOGiqcaENubBZ3J_movCmV6bRUSg(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Hi, I'm trying to find over the entire human genome, for each gene, which exons are the most constitutively expressed. To do this, I'd like to combine expression data (RNA-seq or Microarray) and exons data (UCSC track). Then, for each gene, I'd like to pick the 1 or 2 exons with the highest levels of expression (my proxy for constitutiveness). An additional nicety would be to somehow work in a preference for 5' exons. For example, let's say a gene has 3 exons and, with the expression data, all 3 exons are equally expressed. I'd like to selectively get the first 2 exons. I've started learning Galaxy and was able to import BED files for UCSC exons (as in the Galaxy 101 tutorial) and a BED file for Affy microarray expression data. (I tried also importing the Burge RNA-seq track as BED but couldn't get it to work). I did an inner join on genomic sequences to join the expression data with the exons and sorted them from most expressed to least. But how do I sort within genes? That is, how do I get the top 2 exons per gene (highest expressing exons per gene) and, if there are more than 2 with equally high expression, how do I preferentially get the 5` exons? I'm also open to ways to do this without using Galaxy, etc. I want to do this for an entire genome, so I figured it would be good to have a Galaxy workflow, which I could then apply to other genomes as needed. Thanks for any help

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Finding constitutive exons using expression data
by 7plusorminus 3 09 Feb '14

09 Feb '14

Hi, I'm trying to find over the entire human genome, for each gene, which exons are the most constitutively expressed. To do this, I'd like to combine expression data (RNA-seq or Microarray) and exons data (UCSC track). Then, for each gene, I'd like to pick the 1 or 2 exons with the highest levels of expression (my proxy for constitutiveness). An additional nicety would be to somehow work in a preference for 5' exons. For example, let's say a gene has 3 exons and, with the expression data, all 3 exons are equally expressed. I'd like to selectively get the first 2 exons. I've started learning Galaxy and was able to import BED files for UCSC exons (as in the Galaxy 101 tutorial) and a BED file for Affy microarray expression data. (I tried also importing the Burge RNA-seq track as BED but couldn't get it to work). I did an inner join on genomic sequences to join the expression data with the exons and sorted them from most expressed to least. But how do I sort within genes? That is, how do I get the top 2 exons per gene (highest expressing exons per gene) and, if there are more than 2 with equally high expression, how do I preferentially get the 5` exons? I'm also open to ways to do this without using Galaxy, etc. I want to do this for an entire genome, so I figured it would be good to have a Galaxy workflow, which I could then apply to other genomes as needed. Thanks for any help

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Constitutive exon workflow?
by 7plusorminus 3 08 Feb '14

08 Feb '14

Hi folks, I'm trying to find over the entire human genome, for each gene, which exons are the most constitutively expressed. To do this, I'd like to combine expression data (RNA-seq or Microarray) and exons data (UCSC track). Then, for each gene, I'd like to pick the 1 or 2 exons with the highest levels of expression (my proxy for constitutiveness). An additional nicety would be to somehow work in a preference for 5' exons. For example, let's say a gene has 3 exons and, with the expression data, all 3 exons are equally expressed. I'd like to selectively get the first 2 exons. I've started learning Galaxy and was able to import BED files for UCSC exons (as in the Galaxy 101 tutorial) and a BED file for Affy microarray expression data. (I tried also importing the Burge RNA-seq track as BED but couldn't get it to work). I did an inner join on genomic sequences to join the expression data with the exons and sorted them from most expressed to least. But how do I sort within genes? That is, how do I get the top 2 exons per gene (highest expressing exons per gene) and, if there are more than 2 with equally high expression, how do I preferentially get the 5` exons? I'm also open to ways to do this without using Galaxy, etc. I want to do this for an entire genome, so I figured it would be good to have a Galaxy workflow, which I could then apply to other genomes as needed. Thanks for any help. jim

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How do I remove "Histories shared with you by others"?
by Casey Bergman 06 Feb '14

06 Feb '14

Hello - I am trying to clean out my "Histories shared with you by others" page on the main public Galaxy server. I would like to remove old histories shared with me. I have tried two methods, neither of which allow me to remove these histories: 1. clicking the check box to a history shared with me, then clicking "Unshare" at the bottom of the page 2. clicking the drop down menu and then selecting "Unshare" In both cases, I get the error message "History is not owned by the current user". This behavior appears to be referenced in another recent thread from the sharer's side (http://user.list.galaxyproject.org/Trying-to-quot-unshare-quot-a-history-in…) Any ideas on what is going on here? Best regards, Casey

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Help with Cuffdiff
by Maria Hoffman 06 Feb '14

06 Feb '14

Hello, I am new to cuff diff and just got my data output back and it doesn't look like anything is statistically significant. There are three treatment groups with two biological replicates each group. I am not sure if I made an error somewhere along the line, need to adjust the parameters, or if there really could be no change. The samples are from sheep and I have been using the OvisAries3.0 reference I downloaded from UCSC. Thanks Maria

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Query regarding NCBI BLAST+ blastx
by Deepak Datta 05 Feb '14

05 Feb '14

Hello, I was working with *NCBI BLAST + blastx.*. I have a question regarding one of the columns that reads 'qframe'. When we do Blast on NCBI, we get a column called query coverage. And when we perform NCBI BLAST + blastx, we get 25 columns. I wanted to know which of these columns is analogous to the "query coverage" column. And if these columns do not correspond to "query coverage" then can you kindly let me know how am I supposed to derive that? Looking forward to your response. -- *DD*

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Chip-SEq S.cerevisiae IOn-Torrent
by Mónica Pérez Alegre 04 Feb '14

04 Feb '14

Hi everybody. I´m trying to analyze Chip-SEq Data from Ion-Torrent using Peak Calling/MACS. I have some questions: · How do I establish the Tag size? The median of size reads in my data are 156pb, the max 306? · Bandwidht: is the sonication size? Thanks in advance Regards ☺If you have used the Services of the Genomics Unit of Cabimer, we would be grateful if you would give us a mention in future publications Mónica Pérez Alegre, PhD Genomics Unit CABIMER-CSIC Edif. CABIMER - Avda. Américo Vespucio s/n Parque Científico y Tecnológico Cartuja 93 41092 Seville-SPAIN Tlf: +34 954 467 828 Fax: +34 954 461 664 www.cabimer.es<http://www.cabimer.es/> http://www.cabimer.es/web/es/unidades-apoyo/genomica

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mpileup max coverage
by Wang, Michael 04 Feb '14

04 Feb '14

Hi All, one quick Q: how can I set max per-file depth to more than 8000 under mpileup. Thanks! Michael ________________________________ Email Disclaimer: www.stjude.org/emaildisclaimer Consultation Disclaimer: www.stjude.org/consultationdisclaimer

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Installing tool in galaxy on cloud
by Malik, Shivani 03 Feb '14

03 Feb '14

Hi All, I want to use Tophat2 on amazon cloud. I could not find it in the regular tools unlike the public server. Am I using the right version? I tried installing it through admin on cloud .Though I was able to make myself admin through cloudman instance , I could not see any admin panel on Galaxy main page. What am I doing wrong?Any help is appreciated. Thanks. Shivani

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remove versions of tool
by Ketan Maheshwari 01 Feb '14

01 Feb '14

Hi, I renamed my tool name in <tool name=""> but when I restart Galaxy server, I see a dropdown in front of the tool title with two versions with same value. When I select one it gives current name and when selecting other it gives the older name of the tool. My intention here was to rename the tool and I did not do anything that would tell Galaxy to preserve versions. After looking into the past mailing list posts, I tried to : 1. Restart Galaxy server. 2. Deleted integrated_tool_panel.xml 3. cleared my browser cache and cookies None of the above worked though. Any suggestions? Attached is a snapshot of what I am seeing. Best, -- Ketan

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