Hello,
Yes, MEME is not on the Main server, but can be used in local, cloud, or
slipstream Galaxy installs. For throughput - there are a few
MEME-related repositories in the Tool Shed to choose from. How many
sequences each can process will likely vary and are related to the
hardware the
Dear Galaxy
When running HiSeq shot metagenomics sample from the environment
against megablast and taxonomic representation, How do I filter/remove
all the 16s and other conserved sequences.
The problem if blasting a single organism that has a fraction of
conserved sequence, the results
Hi Brad,
Thanks for the kind reply. So does it mean that I won't be able to add it to
our existing galaxy-dist production server as the only way to obtain it is to
clone the one you listed? Thanks.
Best,
Peter
-Original Message-
From: Brad Chapman [mailto:chapm...@50mail.com]
Sent:
Hello,
I need to perform an action (or series of actions) on an 454 dataset using
Galaxy, and have not been able to figure out the necessary steps, even
after looking through the toolbar expressions and using custom search.
My file is a fasta and has the standard format:
GNJQDEZ01A940A
Hi all,
I would like to analyze my miRNA sequencing analysis from mouse tissue. I
have not any idea which tools or pipeline work best. Do you have any
suggestion?
Regards
Thanh
___
The Galaxy User list should be used for the discussion of
Hello Dominique,
Yes, this can be done. Here is the process -
Start by splitting up the data by using the 'NGS: QC and manipulation -
Barcode Splitter tool. The result files will be available as links.
These can be copied and added to the Get Data - Upload File tool in
the text box, in
Hi Scott,
The tool Metagenomic analyses - Find diagnostic hits can be used to
isolate the conserved sequences. Then, you use the tool Join, Subtract
and Group - Compare to find Non Matching rows of 1st dataset to
filter out anything that you think is spurious for your analysis (put in
Hi Thanh,
Did the Tuxedo suite not work out for you in the end? Or the other tools
that Ross suggested? These are both pipelines that are in common use.
http://lists.bx.psu.edu/pipermail/galaxy-user/2013-July/006367.html
Using a cloud Galaxy and installing tools from the Tool Shed is required
Peter;
Thanks for the kind reply. So does it mean that I won't be able to add
it to our existing galaxy-dist production server as the only way to
obtain it is to clone the one you listed? Thanks.
Unfortunately it's not that easy to graft into place on top of the
existing Galaxy. It requires
Thanks Mete and Jenifer for your information.
Last time, I did mRNA sequencing analysis and decided to go with
TopHatHtseqDESeq for DE genes. Just because the results match up quite
nicely with my qPCR validation. Although Cuufflink/Cuffdiff produced
results with quite similar trend with DESeq,
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