Re: [galaxy-user] copy number variation detcetion in Glaxay

Hello, The tool "FreeBayes" may be of interest. Please see the tool form for links to the primary tool documentation to see if the functionality will meet your needs. Best, Jen Galaxy team On 8/15/12 4:46 AM, shamsher jagat wrote: Is there any tool/ combination of tools with in galaxy whic

[galaxy-user] Cuffdiff errors

Hello, I am having a problem running Cuffdiff on some RNA-seq data. I want to compare 2 samples (A and B). I did Cufflinks and Cuffmerge before running Cuffdiff. I ran Cuffdiff with the following options: Cuffmerge + Bowtie A, B (sorted required by Cufflinks after mapped with Bowtie). But I go

Re: [galaxy-user] copy number variation detcetion in Glaxay

Thanks Jen,   I am also intrested in this. Has any one used FreeBayes in Galaxy or out side Gaaxy to detect CNV from a ilumina sequencing data. Is their a tutorial for running this tools.   Thanks.   From: Jennifer Jackson To: shamsher jagat Cc: galaxy-user@lists.bx.psu.edu Sent: Thursday, A

Re: [galaxy-user] Cuffdiff errors

Hi Yan, Would you please submit this as a bug report? It helps if you leave all inputs undeleted in your history. Instructions: http://wiki.g2.bx.psu.edu/Support#Reporting_tool_errors Thanks! Jen Galaxy team On 8/16/12 6:18 AM, Yan He wrote: Hello, I am having a problem running Cuffdiff o

Re: [galaxy-user] Do I need to allow indel search?

Hello Jianguang, In simple terms, "No" produces a strict alignment and "Yes" produces a more permissive alignment. The option 'Allow indel search:' is a way of allowing for variability in your data (presumably biologically valid) to not be interpreted as mismatches or gaps. Mismatches/gaps i

Re: [galaxy-user] Use Own Junctions or not

Hello Jianguang, Junctions refer to known splice sites. TopHat has several options that work together to supply known junctions and to use them in various ways. This is used to direct splice identification. Given what you have explained about your experiment, I would not think this would be a

Re: [galaxy-user] galaxy-user Digest, Vol 74, Issue 15

o this and other Galaxy lists, > please use the interface at: > >http://lists.bx.psu.edu/ > -- Jennifer Jackson http://galaxyproject.org -- Message: 10 Date: Thu, 16 Aug 2012 21:18:01 +0800 From: Yan He To: Subject: [galaxy-user] Cuffdiff errors Me

[galaxy-user] Counting intervals in one file overlapping intervals in another file - what are the hidden settings?

Hi, I am using the "Count intervals in one file overlapping intervals in another file" tool (part of the bedTools package) to assess the number of RNA-seq reads that map back to a specific region. (I am using this on the Galaxy test server). I am finding that this tool returns many more reads than

[galaxy-user] Minimum length of read segments

Dear All, I am going to run Tophat with RNA-seq dataset to observe alternative splicing events. There is a parameter for Tophat: "Minimum length of read segment". According to "implemented Tophat options", the description for "Minimum length of read segment" is "Each read is cut up into segment

[galaxy-user] run Bowtie to estimate Mean Inner Distance between Mate Pairs

Dear All, In order to figure out the Mean Inner Distance between Mate Pairs of my paired-end RNA-seq datasets, I ran Bowtie (Map with Bowtie for Illumina) with both forward and reverse datasets and mouse mm9 as reference genome. Below I list the Bowtie output for only one pair of reads (I put t

Re: [galaxy-user] copy number variation detcetion in Glaxay

Hi Mathew, To clarify, freebayes is not designed to detect CNVs. It can CNV information detected in another method to correctly genotype at sites with copy number variations. If you have exome data, there is conifer http:// conifer.sourceforge.net/

Re: [galaxy-user] Counting intervals in one file overlapping intervals in another file - what are the hidden settings?

Hello Mo, This tool comes from a repository sourced from the Tool Shed: http://toolshed.g2.bx.psu.edu/ Search for a tool named "bedtools" with owner "aaronquinlan". You could examine the repository and then the tool wrapper author can be contacted directly with questions about parameters or if

Re: [galaxy-user] cuffdiff sample values assigned

Hello, A very similar question came up a few days ago and Jeremy had some good advice for how to approach learning to interpret this data: http://lists.bx.psu.edu/pipermail/galaxy-user/2012-August/004985.html Best, Jen Galaxy team On 8/15/12 8:49 AM, i b wrote: Dear all, in cuffdiff output