User: Elwood Linney

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Elwood Linney180
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3 years, 9 months ago
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5 years, 9 months ago
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Posts by Elwood Linney

<prev • 18 results • page 1 of 2 • next >
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Adding Danrer7 As A Reference Genome For Tophat2
... Can you add danrer7 as a reference genome for tophat2 for online Galaxy? Its there for tophat for Illumina. Elwood Linney ...
galaxy written 3.8 years ago by Elwood Linney180 • updated 3.8 years ago by Jennifer Hillman Jackson23k
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Same Rnaseq Samples Give Different Fpkm Values When Run Against Different Samples
... Hello, I am sure this has come up before and maybe I missed the answer. If in using cuffdiff I run a sample 1(3 repeats) vs a sample 2 and then run the same sample 1(3 repeats) against a sample 3 or a sample 4, I get different value for fpkm from sample 1 each time. Is there something going wrong ...
galaxy written 3.8 years ago by Elwood Linney180 • updated 3.8 years ago by Jennifer Hillman Jackson23k
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Comment: C: Problems In Transitioning From Tophat To Cuffdiff
... thank you all, its clearly working now and that is coming just in time, the results of two of these datasets will help us plan our next experiments for capping up a manuscript or two el linney ...
written 4.1 years ago by Elwood Linney180
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Problems In Transitioning From Tophat To Cuffdiff
... After successfully using RNAseq software in Galaxy online for about 10 different datasets to just get gene expression differences between replicates from control versus exposed zebrafish embryos, I am having no luck getting cuffdiff to work with the "moved" Galaxy. I had this problem with histori ...
cufflinks cuffmerge rna-seq written 4.1 years ago by Elwood Linney180 • updated 4.1 years ago by Jennifer Hillman Jackson23k
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Issues On Rnaseq Since The Changeover
... My histories seem to be stopping their processing around the Tophat-cuffmerge steps since the change over of Galaxy online. Sometimes a red box appears over my history name but disappears in a minute or less. I am wondering, given the way the Toolshed now looks different for RNAseq work, if some c ...
cuffmerge rna-seq written 4.2 years ago by Elwood Linney180 • updated 4.2 years ago by Nate Coraor3.1k
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Problems Processing Histories Existing On Galaxy Before The Changeover
... Is anyone who had developed histories on Galaxy online before the changeover getting red error messages after the changeover for tophat or cuffdiff processing? I have now tried a few times to move forward without luck and will remove at least one of my histories and start all over again just in cas ...
galaxy written 4.2 years ago by Elwood Linney180 • updated 4.2 years ago by Jennifer Hillman Jackson23k
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Online Galaxy Turning Everything Red On Rnaseq Steps
... Hello, I have been waiting a few weeks to process some RNA seq datasets but woke up this morning with lots of steps red. I thought it just might be because of the movement of the system but I processed steps for some histories and everything has turned red. I also noticed that online Galaxy now h ...
galaxy written 4.2 years ago by Elwood Linney180 • updated 4.2 years ago by Jennifer Hillman Jackson23k
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Estimating Galaxy On The Cloud Needs For Rnaseq
... Questions: I have been running sets of data for cufflinks/cuffdiff analysis on Galaxy online--I am considering using the cloud but from what I can read, because of different person's galaxy needs, I can't get an clear idea of what I would need and how long it would take to process (and the cost) if ...
cufflinks rna-seq written 4.2 years ago by Elwood Linney180 • updated 4.2 years ago by Jennifer Hillman Jackson23k
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Portal To Galaxy Restricted
... A message sent earlier this week by me indicated that I could not connect to Galaxy via Fetch to download data. A reply indicated a glitch was fixed. I then could connect with Fetch and I tried to transfer 4 x 16gb files and the connection disconnected about 4 times. Now, once again, I cannot con ...
galaxy written 4.2 years ago by Elwood Linney180 • updated 4.2 years ago by Jennifer Hillman Jackson23k
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Cannot Download Data To Galaxy
... Hello, My connection with Galaxy online shutoff last night while I was transferring data to it. When I tried to connect again with Fetch this morning I was not allowed and a message like "Sorry the maximum number of clients for this user are already connected." I have had what appears to be the ba ...
galaxy written 4.3 years ago by Elwood Linney180 • updated 4.3 years ago by Nate Coraor3.1k

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