User: madkisson

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madkisson30
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30
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New User
Location:
United States
Last seen:
1 year, 4 months ago
Joined:
2 years, 7 months ago
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m********@chori.org

Posts by madkisson

<prev • 43 results • page 1 of 5 • next >
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#{input_name} Doesn't Actually Work
... Hi I've been trying to use the #{input_name} code that is recommended in the workflow editing page [link given is: https://wiki.galaxyproject.org/Learn/AdvancedWorkflow/Variables]. This would save me a great deal of time if i could get it to work. All I ever get is a blank space where that code is ...
tophat workflow written 2.1 years ago by madkisson30 • updated 2.1 years ago by Jennifer Hillman Jackson23k
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Comment: C: exporting dataset (history) or Bam file to another server
... Hey Dannon Yeah sorry about that - I got busy again and didn't follow up. I did what you recommended and kept the export link and continually checked it. It took some time [82 GB history] but it eventually got to where it read 'export is complete' and hit ting the link began a download process. Imp ...
written 2.1 years ago by madkisson30
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Comment: C: exporting dataset (history) or Bam file to another server
... Has there been any progress with this? I'm still trying to move huge histories [~80 GB]  between Galaxy Cloudman clusters and nothing really happens at the Import end. Downloading the history as a compressed file would take 24 hrs, meanwhile the cluster has to be running, costing $$. Will transferri ...
written 2.2 years ago by madkisson30
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TopHat: Raw junction and juncs files
... Hi I'm having a hard time finding information on what exactly the advantage of using the Raw Junction option in TopHat would be. Mostly people just cut and paste the explanation from the TopHat manual. Am I wrong in believing that all this does is take information from one TopHat run and make futur ...
junctions .juncs file tophat written 2.2 years ago by madkisson30 • updated 2.2 years ago by Jennifer Hillman Jackson23k
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Comment: C: TopHat: Error: Couldn't build bowtie index with err = 1
... I should clear something up as well - I'm using this mm10 FASTA file so that I can compare my analysis to that produced by EBI using my same data. We're seeing some differences in output and we want to make sure that all parameters and input are exactly the same. I have no idea what the built in mm1 ...
written 2.3 years ago by madkisson30
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Comment: C: TopHat: Error: Couldn't build bowtie index with err = 1
... Hi Jennifer That didn't seem to work and the error looks pretty much the same. Here's what I had: Master Node Type: c3.2xlarge additional Node Type: m2.2xlarge I watched as things ran for a about 30 minutes. Neither of the nodes maxxed out at any time during the processing that did happen. He ...
written 2.3 years ago by madkisson30
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TopHat: Error: Couldn't build bowtie index with err = 1
... Hi I'm trying to run TopHat on a Cloudman Galaxy instance and I keep getting the below error. I've run TopHat on this FastQ file several times before with great results. the ONLY thing that has changed is that I'm trying to use a Mouse mm10 FastA file [one that has been used elsewhere with success] ...
fasta rnaseq tophat written 2.3 years ago by madkisson30 • updated 2.3 years ago by Jennifer Hillman Jackson23k
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Comment: C: Internal Server Error: Galaxy was unable to successfully complete your request
... I've been getting the same error since yesterday and was told that nobody can deal with it until around 4pm today ...
written 2.4 years ago by madkisson30
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Comment: C: Download From Cloudman via FTP?
... Hi Dannon Have there been any changes on this front? I still haven't found a way to reliably and [reasonably] quickly download 20-40GB of data at a time. Could you go into a little more detail regarding your 'exporting entire histories to archive for download' idea? I've never been able to get the ...
written 2.4 years ago by madkisson30
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Comment: C: cuffdiff & cummerbund
... Oddly enough, a tool called 'CuffDiff for CummeRbund" produces all of the tabular outputs you're looking for and does not produce the sqlite file by default. Go figure ...
written 2.5 years ago by madkisson30

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