User: Nowlan Freese
Nowlan Freese • 860
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Posts by Nowlan Freese
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... I found the [make bam index human readable][1] thread to be very useful for exploring BAI files, especially [Pierre Lindenbaum's][2] tool for [dumping the BAI as XML][3]. In looking at the output of Pierre's tool, it does include the names and lengths of the chromosomes, but they are pulled from the ...
written 9 weeks ago by
Nowlan Freese • 860
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... Thank you John! ...
written 9 weeks ago by
Nowlan Freese • 860
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5 follow
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... Can the chromosome names and lengths to which a bam file was aligned be determined solely from its bai file? ...
written 9 weeks ago by
Nowlan Freese • 860
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Comment:
C: IGV or IGB
... Both projects are currently [funded][1] and actively [developed][2].
[1]: https://projectreporter.nih.gov/project_info_description.cfm?aid=9505926&icde=43356259&ddparam=&ddvalue=&ddsub=&cr=1&csb=default&cs=ASC&pball=
[2]: https://bitbucket.org/lorainelab/integra ...
written 20 months ago by
Nowlan Freese • 860
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... Hi jpere716,
You should be able to view the [depth graph across the entire chromosome][1].
Can you tell me more about the issue you are having? Is the depth graph not loading across the entire chromosome, or is the top of the depth graph being cut off (the height of of the depth graph can be adjus ...
written 20 months ago by
Nowlan Freese • 860
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... 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 4.3 years ago by
Nowlan Freese • 860
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... 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 4.9 years ago by
Nowlan Freese • 860
• updated
10 months ago by
RamRS ♦ 30k
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... 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 ...
written 4.9 years ago by
Nowlan Freese • 860
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... 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 5.2 years ago by
Nowlan Freese • 860
0
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... 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 5.5 years ago by
Nowlan Freese • 860
Latest awards to Nowlan Freese
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2.2 years ago,
created an answer with at least 3 up-votes.
For A: IGB- genome sequence in sequence viewer just shows dashes
Great Question
2.4 years ago,
created a question with more than 5,000 views.
For Video: ChIP-Seq Analysis and Visualization using Galaxy and IGB.
Popular Question
2.4 years ago,
created a question with more than 1,000 views.
For Visualizing protein annotations through ProtAnnot
Great Question
3.6 years ago,
created a question with more than 5,000 views.
For Video: RNA-Seq Alignment and Visualization using Galaxy and IGB
Popular Question
5.3 years ago,
created a question with more than 1,000 views.
For Video: Visualization of whole genome DNA methylation data in IGB
Popular Question
5.4 years ago,
created a question with more than 1,000 views.
For Video: Intro to All New Features in IGB 8.2
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5.5 years ago,
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For A: Where are the different RAM versions of IGB in v8.3.0
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5.6 years ago,
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For A: Where are the different RAM versions of IGB in v8.3.0
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For A: Where are the different RAM versions of IGB in v8.3.0
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For A: Where are the different RAM versions of IGB in v8.3.0
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For (Finished) Live on-line tutorial using Integrated Genome Browser (October 7, 2014 11:30am-12pm EST)
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5.8 years ago,
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For A: Where are the different RAM versions of IGB in v8.3.0
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5.8 years ago,
created an answer that has been accepted.
For A: Where are the different RAM versions of IGB in v8.3.0
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5.8 years ago,
created an answer with at least 3 up-votes.
For A: IGB- genome sequence in sequence viewer just shows dashes
Appreciated
5.8 years ago,
created a post with more than 5 votes.
For (Finished) Live on-line tutorial using Integrated Genome Browser (October 7, 2014 11:30am-12pm EST)
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5.8 years ago,
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For (Finished) Live on-line tutorial using Integrated Genome Browser (November 12, 2014 11:30am-12pm EST)
Popular Question
5.8 years ago,
created a question with more than 1,000 views.
For (Finished) Live on-line tutorial using Integrated Genome Browser (November 12, 2014 11:30am-12pm EST)
Appreciated
5.9 years ago,
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For (Finished) Live on-line tutorial using Integrated Genome Browser (October 7, 2014 11:30am-12pm EST)
Popular Question
5.9 years ago,
created a question with more than 1,000 views.
For Finished - Live on-line tutorial using Integrated Genome Browser (November 12, 2014 11:30am-12pm EST)
Teacher
5.9 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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6.0 years ago,
created a post with more than 5 votes.
For (Finished) Live on-line tutorial using Integrated Genome Browser (October 7, 2014 11:30am-12pm EST)
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6.1 years ago,
created a post with more than 5 votes.
For (Finished) Live on-line tutorial using Integrated Genome Browser (October 7, 2014 11:30am-12pm EST)
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