User: Nowlan Freese

gravatar for Nowlan Freese
Nowlan Freese810
Reputation:
810
Status:
Trusted
Location:
United States
Last seen:
3 months ago
Joined:
2 years, 11 months ago
Email:
n************@gmail.com

Posts by Nowlan Freese

<prev • 23 results • page 1 of 3 • next >
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Comment: C: IGB doen't recognize all the peaks
... Hi Iraia, Were you able to figure out the issue? If not, can you send me an image or an example of the data? Nowlan ...
written 13 months ago by Nowlan Freese810
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Comment: C: Video: Visualization of whole genome DNA methylation data in IGB
... Hi Dr. Franco, The methods that have been recommended to me for analyzing methylation data can be found in two papers: "Human body epigenome maps reveal noncanonical DNA methylation variation" and "Charting a dynamic DNA methylation landscape of the human genome". The supplementary information goes ...
written 20 months ago by Nowlan Freese810
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Tutorial: Visualizing protein annotations through ProtAnnot
... Interested in finding out how to visualize protein annotations in the context of genomic sequence?  Look for the Integrated Genome Browser at the international Plant and Animal Genome 2016 meeting in San Diego. The IGB team will be giving a live computer demo of the many features in IGB, including ...
annotation tutorial protein igb rna-seq written 20 months ago by Nowlan Freese810
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Answer: A: Is it possible to load export files from AncestryDNA into IGB?
... Hi drmoose94, Yes, it is possible to load the raw data files from AncestryDNA into IGB. You will need to convert the raw data into BED detail format first (https://genome.ucsc.edu/FAQ/FAQformat.html#format1.7), and then you can drag and drop the file directly into IGB. So here's what my original d ...
written 2.0 years ago by Nowlan Freese810
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Comment: C: Video: Alternative Splicing and Primer Design
... Hi Pengcheng Yang, There is currently no way to design primers from within IGB. My advice would be to use IGB to identify regions of alternative splicing, and then use primer 3 to pick primers. 1) Identify alternative splicing event of interest in IGB. 2) Copy the DNA sequence directly from IGB a ...
written 2.3 years ago by Nowlan Freese810
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Answer: A: Can IGB load BED 6+3 files?
... Hi pgarcia, The .broadPeak format is not a currently supported file format in IGB, however it can easily be converted to the more common .bed format, which is supported.   To convert the file to a bed file, limit the data to the first 6 columns.  To do this on the command line use: $cut –f1-6 FILE ...
written 2.3 years ago by Nowlan Freese810
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Answer: A: How to optimize stack height of .wig files in IGB
... Hi Sarah, The .wig files are considered graphs in IGB. The equivalent to optimizing stack height for a graph file would be to adjust the Y-axis of the graph so that it is displaying all of the data. 1) Highlight the .wig file track 2) Click on the Graph tab 3) Drag the rightmost slider under the ...
written 2.3 years ago by Nowlan Freese810
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Answer: A: IGB Genome Version ce10: WS140 or WS220?
... Hi smpyonteck, The C. elegans genome version in IGB "C_elegans_Oct_2010" is the most recent version, i.e. WS220/ce10. The title within the browser "WS140/ce10" is a typo in our synonym file. Thank you for finding this! Nowlan ...
written 2.4 years ago by Nowlan Freese810
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Answer: A: Regulatory motif analysis in Integrated Genome Browser
... Hi nkm34, The first thing that comes to mind would be to use the Advanced Search function in IGB to search for your specific motifs. 1. Click on the Advanced Search tab. 2. Select Residues under the Search dropdown menu. 3. Enter your motif(s) - we support use of regular expressions and wild car ...
written 2.4 years ago by Nowlan Freese810
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Answer: A: How About Starting A Tutorial For Chip Seq Data Analysis?
... Here's a video tutorial on ChIP-seq using Galaxy for data analysis and IGB to visualize the results: https://www.biostars.org/p/126760/ ...
written 2.4 years ago by Nowlan Freese810

Latest awards to Nowlan Freese

Great Question 5 months ago, created a question with more than 5,000 views. For Video: RNA-Seq Alignment and Visualization using Galaxy and IGB
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Video: Visualization of whole genome DNA methylation data in IGB
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Video: Intro to All New Features in IGB 8.2
Scholar 2.3 years ago, created an answer that has been accepted. For A: Where are the different RAM versions of IGB in v8.3.0
Scholar 2.4 years ago, created an answer that has been accepted. For A: Where are the different RAM versions of IGB in v8.3.0
Supporter 2.4 years ago, voted at least 25 times.
Appreciated 2.4 years ago, created a post with more than 5 votes. For A: Where are the different RAM versions of IGB in v8.3.0
Scholar 2.4 years ago, created an answer that has been accepted. For A: Where are the different RAM versions of IGB in v8.3.0
Good Answer 2.6 years ago, created an answer that was upvoted at least 5 times. For A: Where are the different RAM versions of IGB in v8.3.0
Scholar 2.6 years ago, created an answer that has been accepted. For A: Where are the different RAM versions of IGB in v8.3.0
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: IGB- genome sequence in sequence viewer just shows dashes
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: IGB- genome sequence in sequence viewer just shows dashes

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