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 which
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
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 j...@bx.psu.edu
To: shamsher jagat kanwar...@gmail.com
Cc:
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
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 in
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
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Message: 11
Date: Thu, 16 Aug 2012 08:09:15 -0700
From: Jennifer Jackson j...@bx.psu.edu
To: Yan He yanh
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
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 segments,
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
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://http://conifer.sourceforge.net/
conifer.sourceforge.net/
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