User: vaughandy

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vaughandy10
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Posts by vaughandy

<prev • 12 results • page 1 of 2 • next >
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stringtie output from multiple samples into an FPKM matrix
... Hi all, Anyone have a good set of steps to take the stringtie transcript-level expression output from multiple samples and put it into an FPKM matrix? Do I need to first normalize between the samples with something like cuffmerge? I thought that Stringtie merge would do this, but it doesn't seem ...
stringtie fpkm merge written 8 months ago by vaughandy10 • updated 8 months ago by Mo Heydarian790
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instructions for fetching and install mm10 genome and hisat indexing for local galaxy
... Hi all, Is there a kind soul that could take me through a step-by-step of fetching and indexing the mouse mm10 genome from UCSC (or wherever) on a local galaxy install, with a data manager? I have the indexers installed as well as create db key, rsync, and fetch reference genome. I just can't see ...
hisat2 index refererence genome written 9 months ago by vaughandy10 • updated 9 months ago by Jennifer Hillman Jackson23k
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hisat2 index issue (I think)
... Hi all, I used the hisat2 index builder data manager to create a hisat2 reference for a local galaxy server I set up. It ran successfully and now shows up as a built-in genome when running hisat2 and in the "hisat2 indexes" data table entry. However, every time I try to perform an alignment, it i ...
hisat2 index hisat reference genome written 9 months ago by vaughandy10
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can't access data managers
... Hi, I'm trying to use Data Managers to add my own built-in reference genomes for Hisat on a local install of Galaxy (i.e. http://bioinformatics.ucdavis.edu/research-computing/documentation/using-datamanagers-to-create-your-own-built-in-genomes/) Frustratingly, I can't find the "Manage Local Data" ...
reference genomes data manager written 10 months ago by vaughandy10 • updated 10 months ago by fubar1.1k
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Answer: A: HISAT2 path problem (I think)
... Hi all, Thanks for your help. I finally got this to work by adding the samtools path to the /etc/sudoers file under the "secure path" section. Thanks!! ...
written 10 months ago by vaughandy10
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Answer: A: HISAT2 path problem (I think)
... This is incredibly frustrating. I keep getting this same error. I know I've added samtools to PATH, when I open a terminal and type samtools it works fine. everything else is working fine. i noticed if I type sudo samtools, then it doesn't work. i'm running the server with the sudo command. so ...
written 10 months ago by vaughandy10
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Comment: A: HISAT2 path problem (I think)
... I'm using the default config. Not sure about the rest of that, I'm just a newby. All I can say is I've been able to install and run a local instance of galaxy, as well as install a few tools (fastq groomer, hisat, cufflinks). ...
written 10 months ago by vaughandy10
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HISAT2 path problem (I think)
... Hi all, Running a local install of Galaxy and HISAT2 keeps spitting back the following error when it's done: OSError: [Errno 2] No such file or directory From googling around I think it's a problem with adding samtools to PATH, but for the life of me nothing I try seems to correct it. I'm runnin ...
hisat2 samtools ubuntu path written 10 months ago by vaughandy10 • updated 10 months ago by Jennifer Hillman Jackson23k
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Answer: A: maximize system resources available to local galaxy server
... The particular processes I would like to run with the most access to system resources are HISAT2, FASTQ groomer, and Cufflinks. ...
written 11 months ago by vaughandy10
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maximize system resources available to local galaxy server
... Hi all, I wonder if someone can suggest how best to give galaxy all the resources I can on a local install running on Ubuntu. Should I be editing the "job_resouce_params_conf" file? Other things to do? My install seems to be running okay, but I'd like to make sure I'm taking advantage of all the ...
resouces galaxy written 11 months ago by vaughandy10

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