User: Chris Whelan
Chris Whelan • 540
- Reputation:
- 540
- Status:
- Trusted
- Location:
- Portland, OR
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- Google Scholar Page
- Last seen:
- 2 years, 3 months ago
- Joined:
- 7 years, 9 months ago
- Email:
- c******@gmail.com
Posts by Chris Whelan
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... You should be able to just use the --excludeNonVariants flag for GATK SelectVariants. ...
written 2.4 years ago by
Chris Whelan • 540
1
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5
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3.3k
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5
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... You should be able to just use the --excludeNonVariants flag for GATK SelectVariants. ...
written 2.4 years ago by
Chris Whelan • 540
1
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6
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9.1k
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6
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... This paper offers an evaluation of four commonly used tools (XHMM, ExomeDepth, CoNIFER, and CONTRA). The results show how hard a problem it is:
http://onlinelibrary.wiley.com/doi/10.1002/humu.22537/abstract
...
written 4.6 years ago by
Chris Whelan • 540
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... This is similar to a question I asked a while back (and never really found an answer for..) Need advice on the correct usage for the Genome Structure Correction statistical software from the ENCODE project
...
written 4.8 years ago by
Chris Whelan • 540
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3
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5.3k
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3
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... You could also use the fuzznuc tool from the EMBOSS suite for this:
http://emboss.sourceforge.net/apps/cvs/emboss/apps/fuzznuc.html
...
written 4.9 years ago by
Chris Whelan • 540
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2
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... Insertions are also more difficult to find because you can't use the paired-end mapping technique if the insertion is too long. If two reads in a pair come from either side of a deletion, you can identify the deletion by looking for a longer distance between mappings of paired reads than you'd expec ...
written 4.9 years ago by
Chris Whelan • 540
2
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17
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17
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... A new one I think is:
BioDatomics -- http://www.biodatomics.com/
...
written 5.1 years ago by
Chris Whelan • 540
2
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4
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4
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... It looks like ChIPModule is designed to do that:
http://hulab.ucf.edu/research/projects/ChIPModule/index.html
Also, I think that Homer can help with this, although I've only used it for finding enriched motifs, rather than co-enriched motifs. It was very straightforward to use for the simpler task ...
written 5.2 years ago by
Chris Whelan • 540
2
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1
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1.3k
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1
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... You could also look at SEAL:
http://biodoop-seal.sourceforge.net/
My structural variation detection too, Cloudburst, also has commands to parallelize mappings in Hadoop:
https://github.com/cwhelan/cloudbreak
...
written 5.2 years ago by
Chris Whelan • 540
0
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2
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5.0k
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... Yes, I've used this strategy too, and it worked well.
...
written 5.4 years ago by
Chris Whelan • 540
Latest awards to Chris Whelan
Supporter
4.7 years ago,
voted at least 25 times.
Teacher
4.9 years ago,
created an answer with at least 3 up-votes.
For A: Why Insertion Are Hard To Find By The Alignments Of Reads Than Deletion ?
Teacher
6.2 years ago,
created an answer with at least 3 up-votes.
For A: What Type Of Information Does The Data Downloaded From The 1000 Genomes Contain?
Good Answer
6.2 years ago,
created an answer that was upvoted at least 5 times.
For A: What Type Of Information Does The Data Downloaded From The 1000 Genomes Contain?
Appreciated
6.2 years ago,
created a post with more than 5 votes.
For A: What Type Of Information Does The Data Downloaded From The 1000 Genomes Contain?
Student
6.6 years ago,
asked a question with at least 3 up-votes.
For Need Advice On The Correct Usage For The Genome Structure Correction Statistical Software From The Encode Project
Good Question
6.6 years ago,
asked a question that was upvoted at least 5 times.
For Need Advice On The Correct Usage For The Genome Structure Correction Statistical Software From The Encode Project
Popular Question
6.6 years ago,
created a question with more than 1,000 views.
For Need Advice On The Correct Usage For The Genome Structure Correction Statistical Software From The Encode Project
Appreciated
6.6 years ago,
created a post with more than 5 votes.
For Need Advice On The Correct Usage For The Genome Structure Correction Statistical Software From The Encode Project
Teacher
6.7 years ago,
created an answer with at least 3 up-votes.
For A: Why Does Chip-Seq Data Have Lots Of Reverse-Complement Pairs Of Reads?
Teacher
7.8 years ago,
created an answer with at least 3 up-votes.
For A: What Tools/Libraries Do You Use To Visualize Genomic Feature Data?
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