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Search: Posts Made By: gkuffel
Forum: Bioinformatics 07-28-2017, 10:50 AM
Replies: 1
Views: 1,101
Posted By gkuffel
Tools for Enrichment Analysis

Hi everyone,

I manage a NGS core and I am a Bioinformatician by training. I use my favorite tool DESeq2 for all of my differential expession analysis. Many users are asking for enrichment...
Forum: Bioinformatics 06-15-2017, 08:36 AM
Replies: 1
Views: 551
Posted By gkuffel
Read mapping to mir-21a in a mir-21 Knock-out mouse

Hoping the community can provide some insight. I manage a NGS core facility and recently did some miRNA-Seq for a user. The library kit was NEB Next Small RNA and I sequenced on the MiSeq generating...
Forum: Bioinformatics 05-17-2017, 08:30 AM
Replies: 1
Views: 1,059
Posted By gkuffel
Bowtie to analyze miRNA

Hi everyone,

I have 50 bp single end miRNA reads from mouse generated on the MiSeq. So far I have trimmed adapters using Cutadapt and now I am mapping to the whole genome using Bowtie. After...
Forum: Bioinformatics 10-27-2016, 08:23 AM
Replies: 2
Views: 1,507
Posted By gkuffel
Bowtie2 for miRNA-Seq

Hopefully someone can help. I have read conflicting info about aligners for miRNA data but I have finally decided on Bowtie2. I have 3 questions:

1. Can anyone share the parameters they are using...
Forum: Bioinformatics 08-25-2016, 11:21 AM
Replies: 1
Views: 1,942
Posted By gkuffel
Bash script to automate htseq-count

Hi everyone-

I am trying to write a script to automate htseq-count on a large number of samples. The script runs but then throws the following error: "Please provide 2 arguments". Does anyone see...
Forum: Core Facilities 09-30-2015, 09:20 AM
Replies: 4
Views: 4,287
Posted By gkuffel
The Best Robot for NGS Library Prep

Hi everyone,

I wanted to get some insight on a robot for NGS library prep. I am a Lab Mgr. of a NGS core that currently runs 2 MiSeqs. So far we have been considering the EpMotion 5075 but it is...
Forum: Core Facilities 09-30-2015, 09:15 AM
Replies: 1
Views: 2,864
Posted By gkuffel
The Best Robot for DNA Extractions

Hi Everyone,

I am the Lab Mgr of a NGS Core Facility and we are in the market for a robot to perform DNA and RNA extractions. I have looked at the QIACube and Promega's Maxwell so far but I am...
Forum: Bioinformatics 02-09-2015, 01:22 PM
Replies: 12
Views: 1,082
Posted By gkuffel
I finally understand what you mean. Thanks for...

I finally understand what you mean. Thanks for your patience. Here is my new command:

tophat --GTF home/gkuffel/Workflowfolder/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf --library-type...
Forum: Bioinformatics 02-09-2015, 12:34 PM
Replies: 12
Views: 1,082
Posted By gkuffel
The file from igenomes is: ...

The file from igenomes is:

Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf

I have transferred the entire folder for Mus_musculus to our server.

S1.fastq is my data.

I don't think that...
Forum: Bioinformatics 02-09-2015, 12:05 PM
Replies: 12
Views: 1,082
Posted By gkuffel
That is exactly where I got the genome that I am...

That is exactly where I got the genome that I am using. I used the FTP site to transfer the file to my computer and then I used FUGU to get the file to my account on our server that I use to run...
Forum: Bioinformatics 02-09-2015, 11:52 AM
Replies: 12
Views: 1,082
Posted By gkuffel
Hmm, I guess I am not understanding then. I am...

Hmm, I guess I am not understanding then. I am calling tophat from a terminal window. We have a cluster that I ssh into. I have an account that lives on the server. I am calling tophat from a folder...
Forum: Bioinformatics 02-09-2015, 10:45 AM
Replies: 12
Views: 1,082
Posted By gkuffel
Thank you for taking the time to help. I am...

Thank you for taking the time to help. I am familiar with Unix conventions. I am calling tophat from the directory that contains the fastq file so the file name should be the correct path. I don't...
Forum: Bioinformatics 02-09-2015, 09:05 AM
Replies: 12
Views: 1,082
Posted By gkuffel
Issues with Tophat

Hi All-

I am analyzing RNASeq data for the first time using Tophat and when I run the following command through the terminal the Tophat information/help page pops up and nothing else seems to...
Forum: Illumina/Solexa 04-15-2014, 11:18 AM
Replies: 0
Views: 857
Posted By gkuffel
cBot Reagent HT1

Hi all,

Can anyone tell me exactly how HT1 (Hybridization Buffer), on a biochemical level, aids in binding the template DNA to the flow cell. Thank you in advance.
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