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User: Chris Whelan

gravatar for Chris Whelan
Chris Whelan • 550
Reputation:
550
Status:
Trusted
Location:
Portland, OR
Scholar ID:
Google Scholar Page
Last seen:
3 years, 11 months ago
Joined:
9 years, 5 months ago
Email:
c******@gmail.com

Posts by Chris Whelan

<prev • 35 results • page 1 of 4 • next >
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Answer: A: Remove positions that are non-variant in a subset of samples from a vcf file
... You should be able to just use the `--excludeNonVariants` flag for GATK SelectVariants. ...
written 4.0 years ago by Chris Whelan • 550 • updated 3 months ago by RamRS ♦ 28k
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Answer: A: CNV analysis tool on exome data for NGS
... 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 6.3 years ago by Chris Whelan • 550 • updated 7 months ago by RamRS ♦ 28k
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Comment: C: Interpreting Genome_Structural_Correction Block_Bootstrap.Py
... 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 6.4 years ago by Chris Whelan • 550
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Answer: A: How Do I Search A Genome For A Known Motif, And Get An Interval File Of All Inst
... You could also use the fuzznuc tool from the EMBOSS suite for this: http://emboss.sourceforge.net/apps/cvs/emboss/apps/fuzznuc.html ...
written 6.5 years ago by Chris Whelan • 550
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Answer: A: Why Insertion Are Hard To Find By The Alignments Of Reads Than Deletion ?
... 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 6.6 years ago by Chris Whelan • 550
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Answer: A: List Of Cloud Genomics Companies
... A new one I think is: BioDatomics -- http://www.biodatomics.com/ ...
written 6.7 years ago by Chris Whelan • 550
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Answer: A: Tool Or Technique To Find Co-Occuring Motifs Within Genomic Intervals That Corr
... 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 6.9 years ago by Chris Whelan • 550
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Answer: A: Mapping Applications On Hadoop Cluster
... 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 6.9 years ago by Chris Whelan • 550
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Comment: C: Publicly Available Pipeline For Analysis Of Whole Genome Bisulfite Sequencing Da
... Yes, I've used this strategy too, and it worked well. ...
written 7.1 years ago by Chris Whelan • 550
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Answer: A: Pybedtools - Intersect Only Certain Feature Types
... You can use pybedtools filters to get the right intervals out (untested code): def insertion_filter(feature): return feature[7] == 'INS' ab = a.filter(insertion_filter).intersect(b.filter(insertion_filter), f=0.9, r=False) The second part of your question (reporting intersections that don't ...
written 7.1 years ago by Chris Whelan • 550

Latest awards to Chris Whelan

Supporter 6.3 years ago, voted at least 25 times.
Teacher 6.6 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 7.8 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 7.8 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 7.8 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 8.2 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 8.2 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 8.2 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 8.2 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 8.4 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 9.5 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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