User: gkuffel22

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gkuffel22140
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140
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Laboratory Mgr. at Loyola Genomics Facility, providing a cost effective sample to data solution.

Posts by gkuffel22

<prev • 37 results • page 1 of 4 • next >
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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 10 days ago by gkuffel22140
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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 14 months ago by gkuffel22140 • updated 14 months ago by Jennifer Hillman Jackson21k
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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 17 months ago by gkuffel22140 • updated 17 months ago by Jennifer Hillman Jackson21k
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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 18 months ago by gkuffel22140
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More Problems with Cuffdiff
... Hope someone can help, I have some RNASeq data and I have 2 groups (Control and Treatment) each containing 3 replicates. When I run Cuffdiff just as proof of concept I ran the groups (Control and Treatment) with one sample in each group. This worked great, the gene names were assigned and there wer ...
cuffdiff written 18 months ago by gkuffel22140
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Comment: C: Error in CuffDiff
... Jen, This will not help me as fasta files and gff files for micro RNA are not available through igenomes. Other people are using CuffDiff for miRNA analysis so there must be another way. Thanks for your help. ...
written 20 months ago by gkuffel22140
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Issues with Using CuffDiff Tool in Galaxy
... Hi,   I am analyzing microRNASeq data. My pipeline is qc reads, bowtie for alignment, cufflinks to assemble transcripts, and cuffdiff to get differential expression. Here is my problem, I KNOW that cuffdiff requires a gff/gtf file in a certain format. I got my gff3 from miRBase and it corresponds ...
cuffdiff micrornaseq gff3 written 20 months ago by gkuffel22140 • updated 20 months ago by Jennifer Hillman Jackson21k
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Error in CuffDiff
... I would be forever grateful if someone could take the time to help me. I am attempting to analyze micro RNASeq data. I downloaded the microRNA sequences from miRBase and mapped my samples (fastq files) using Bowtie. After this, I ran flagstat to check the alignments. The alignments looked great, 75% ...
cuffdiff micrornaseq cufflinks gff3 mirbase written 22 months ago by gkuffel22140 • updated 21 months ago by Jennifer Hillman Jackson21k
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How to determine your reference fasta and gtf file match?
... I know I have asked this question before and the solution seems simple but I really do not understand how to tell if my reference fasta file and gtf file are compatible so that when I run Cufflinks gene id's will be populated with actual gene names. If I get a reference fasta (i.e. hg19) and a gtf f ...
mirnaseq cufflinks written 22 months ago by gkuffel22140
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Error in Downloading Tool to Local Galaxy
... Hi, I am trying to download some new tools for microRNA expression analysis such as cutadapt and miRDeep2, however these tools have dependencies on Perl 5.18 and no matter what I try I cannot get Perl to install. Here are the errors I am seeing when I try to download Perl: Name Version ...
software error perl written 22 months ago by gkuffel22140

Latest awards to gkuffel22

Popular Question 13 months ago, created a question with more than 1,000 views. For Uploading multiple FastQ files from BaseSpace to Galaxy
Popular Question 13 months ago, created a question with more than 1,000 views. For Trimming Adapters for Illumina Small RNA Libraries
Autobiographer 14 months ago, has more than 80 characters in the information field of the user's profile.
Student 22 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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