User: gkuffel22

gravatar for gkuffel22
gkuffel22170
Reputation:
170
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Location:
United States
Last seen:
3 days, 3 hours ago
Joined:
2 years, 2 months ago
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Laboratory Mgr. at Loyola Genomics Facility, providing a cost effective sample to data solution.

Posts by gkuffel22

<prev • 43 results • page 1 of 5 • next >
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Running DESeq2 inside local Galaxy instance
... We have tried many times to install DESeq2 to our local instance of Galaxy. The install is successful but when we run the tool we get the following error: Fatal error: An undefined error occurred, please check your input carefully and contact your administrator. Error in library("getopt") : ther ...
deseq2 galaxy bioconductor written 3 days ago by gkuffel22170
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Answer: A: Remove genomes from tool drop down menus
... I wanted to add that I have since figured this out. It turns out that when I utilized the data managers in an attempt to upload reference genomes they were adding information to .loc files in a different location than specified in the instructions for manually adding genomes. Once I found these and ...
written 5 days ago by gkuffel22170
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Issue installing Galaxy on a local server for a multi-user production environment
... Hi everyone, We are installing Galaxy on our local server for a multi-user production environment using: **git clone -b release_17.01 https://github.com/galaxyproject/galaxy.git** The error we get is: **./scripts/common_startup.sh: line 122: .venv/bin/activate: No such file or directory** Can ...
galaxy software error written 5 days ago by gkuffel22170 • updated 5 days ago by Martin Čech ♦♦ 3.8k
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Using Cufflinks v. 2.2.1.5
... Hello community, Let me lead with, I have never been able to successfully run the tophat2-cufflinks-cuffmerge-cuffdiff pipeline before and actually end up with non-zero values populated in the log-fold change column AND get gene names as I show a screenshot below, so as you can imagine it is a good ...
cuffdiff cufflinks cuffmerge rna-seq written 18 days ago by gkuffel22170 • updated 5 days ago by Martin Čech ♦♦ 3.8k
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Remove genomes from tool drop down menus
... I really hope someone can help. I have a local instance of Galaxy. I have genomes that appear in my dropdown box for Bowtie2 that I never added. These genomes are not in the Bowtie2.indices.loc file, so where are they coming from? This is driving me crazy, I have looked everywhere but can't seem to ...
genomes bowtie2 galaxy written 27 days ago by gkuffel22170
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Can't Rsync bacterial genomes
... Hi everyone, I have a local instance of Galaxy. I am trying to grab some of the reference genomes as they appear on the public instance. I have successfully downloaded Rat and PhiX using the Rsync command. Could someone tell me why I cannot grab other bacterial genomes like Staph aureus. I used th ...
genomes rsync galaxy written 27 days ago by gkuffel22170 • updated 24 days ago by Jennifer Hillman Jackson22k
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Comment: C: Cannot add hg19 reference genome to bowtie2 on galaxy
... Hi there, I realize this post is really old but I am desperately trying to manually add genomes into my local Galaxy instance. Specifically, I have done exactly as you did above. I have modified my ~/galaxy-dist/tool-data/bowtie2_indices.loc and the reference genome is added to the builds.txt file. ...
written 5 weeks ago by gkuffel22170
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Uploading fastq files
... Hi, This will be an easy one...when uploading fastq files to Galaxy is it important to associate a Database/Build with each sample and why?  Thank you in advance. ...
galaxy written 15 months ago by gkuffel22170 • updated 15 months ago by Jennifer Hillman Jackson22k
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Trimming Adapters for Illumina Small RNA Libraries
... Does anyone know exactly which sequences I should be clipping on an Illumina Small RNA library before aligning? I have the Illumina Adapter letter which specifies the following but I am not sure if I just type these in as seen or if I need to take the reverse complement of the sequences: TruSeq® Sm ...
mirnaseq written 18 months ago by gkuffel22170 • updated 18 months ago by Jennifer Hillman Jackson22k
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Comment: C: More Problems with Cuffdiff
... Hi Jen, Thank you for taking the time to help me. This work was initially done on our local instance of Galaxy but I reproduced the work on http://usegalaxy.org and the result is the same. Here is a history link: https://usegalaxy.org/u/gina22/h/luthertest. ...
written 19 months ago by gkuffel22170

Latest awards to gkuffel22

Scholar 5 days ago, created an answer that has been accepted. For A: Remove genomes from tool drop down menus
Popular Question 18 days ago, created a question with more than 1,000 views. For Adding reference genomes to local instance of Galaxy using Rsync
Popular Question 14 months ago, created a question with more than 1,000 views. For Uploading multiple FastQ files from BaseSpace to Galaxy
Popular Question 14 months ago, created a question with more than 1,000 views. For Trimming Adapters for Illumina Small RNA Libraries
Autobiographer 15 months ago, has more than 80 characters in the information field of the user's profile.
Student 23 months ago, asked a question with at least 3 up-votes. For Creating a Workflow for Variant Detection for 200 samples

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