User: tymiller

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tymiller60
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New User
Location:
United States
Last seen:
1 year, 8 months ago
Joined:
3 years, 2 months ago
Email:
t*******@case.edu

Posts by tymiller

<prev • 12 results • page 1 of 2 • next >
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Comment: C: Finding a public galaxy instance with a specific tool
... I completely agree! I've been trying to use computeMatrix with plotProfile in combination to do something similar, but I can't get the same outputs. The collaborator who told me to use this is at the Broad, and they and their colleagues use it all the time in command line. I'm trying to get Pol2 ...
written 22 months ago by tymiller60
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Comment: C: Finding a public galaxy instance with a specific tool
... That is so helpful!! I had no idea it would be that easy to create my own galaxy instance. Works great, thanks! ...
written 22 months ago by tymiller60
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Comment: C: Finding a public galaxy instance with a specific tool
... So here is the issue. I'm pretty sure the most common reference genomes were installed when the cloudman galaxy instance was created - including hg19. However the tool doesn't recognize them as being available (the place to select the reference genome doesn't give a dropdown menu, you can just type ...
written 22 months ago by tymiller60
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Comment: C: Finding a public galaxy instance with a specific tool
... NGS.plot It's a tool I installed from the toolshed https://toolshed.g2.bx.psu.edu/repository?repository_id=1838f2840adb4f23&changeset_revision=f7debdafc7cb ...
written 22 months ago by tymiller60
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Answer: A: Finding a public galaxy instance with a specific tool
... Hi Mohammad, Do you know if the CloudMan Galaxy instance comes installed with reference genomes (specifically hg19)? I keep getting an error with this tool that seems like it can't find a dataset it needs, but I've given it everything else. I can't find anywhere that galaxy lists the reference gen ...
written 22 months ago by tymiller60
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Answer: A: Need help with "Count intervals in one file overlapping intervals in another fil
... Hi, I also had a question with this tool. A clarification really. This counts overlaps (in my case from a BAM file overlapping a bed file loci). How is the overlap counted? Is it any read in the BAM file (input A) that overlaps the loci (input B) by at least 1 bp? The other question: is every l ...
written 22 months ago by tymiller60
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Comment: A: Finding a public galaxy instance with a specific tool
... Thanks for the response Martin! Unfortunately, I was not able to see what that link allowed me to do, as it did not lead to a usable tool - it was only an output of three columns and one row. Is it something I can use to find if this tool is installed on a particular public instance, even if one ...
written 22 months ago by tymiller60
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Finding a public galaxy instance with a specific tool
... Hi, I've had this question several times over the last couple of years - is there a way to find a public galaxy instance that contains a specific tool that I would like to use? I would really like to use NGS.plot on galaxy. It has been place in the tool shed https://toolshed.g2.bx.psu.edu/reposito ...
chip-seq ngs.plot written 22 months ago by tymiller60
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Count intervals in one file overlapping intervals in another file -No longer available?
... Hi,  I have used the 'Count intervals in one file overlapping intervals in another file' tool from BedTools many times now and it works great to calculate the RPKM values for loci in ChIP-seq data.  However, it no longer seems to be available on the UseGalaxy Instance.  Is this correct? Did somethi ...
bedtools written 24 months ago by tymiller60 • updated 24 months ago by Jennifer Hillman Jackson24k
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Comment: C: Need help with "Barcode Splitter" tool
... I used visual basic and this was code Sub ExtractHL() Dim HL As Hyperlink For Each HL In ActiveSheet.Hyperlinks HL.Range.Offset(0, 1).Value = HL.Address Next End Sub ...
written 2.6 years ago by tymiller60

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