Dear Galaxy users,
Has anyone experienced this problem before? In my local instance of Galaxy on a
server I've deleted the path of almost all sections with their corresponding
tools from tool_conf.xml (wanting to leave my own customized section) but after
a restart and a new run of the run.sh
moving to galaxy-dev
this is probably related to this issue:
http://dev.list.galaxyproject.org/problems-with-labels-in-the-tool-box-and-order-of-the-tools-td4655985.html
Hence, try deleting integrated_tool_panel.xml first before you do a
restart.
Regards, Hans
On 09/06/2012 01:29 PM,
Dear All,
I am not so sure about two Tophat settings. Please help.
1) Number of mismatches allowed in the initial read mapping
Based on the documantation, my understanding is: the reads are re-aligned to
transcriptome/genome if the mismatches in the initial alignment is more than
the set
Hello Jianguang,
Fold is included in the Cuffdiff output. Section Differential
expression tests, first file, column #9.
http://cufflinks.cbcb.umd.edu/manual.html
Hopefully this helps,
Jen
Galaxy team
On 9/4/12 1:16 PM, Du, Jianguang wrote:
Dear All,
I am looking for the differential
Hi Jen,
Thank you for your answer.
However, the output file transcript differential expression testing gives the
ratio (log2 of the fold change) of FPKM of a specific transcript between two
conditions, which means this fold change in FPKM does not take the overall gene
expression into
Dear All,
I tested how to set the Number of mismatches allowed in the initial read
mapping as follows.
At first, I ran FASTQ Groomer on a dataset to get the number of total reads.
The total number of the reads is 17510227.
Then I ran Tophat after set Number of mismatches allowed in the
6 matches
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