User: Collin

gravatar for Collin
Collin850
Reputation:
850
Status:
Trusted
Location:
United States
Last seen:
9 hours ago
Joined:
5 years ago
Email:
c************@gmail.com

Posts by Collin

<prev • 97 results • page 1 of 10 • next >
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Comment: C: Variant Calling scRNA-seq data for KRAS mutations
... Yes, you are right. But there are also oncogenes that may have many mutations in the middle of a long protein and might not get any coverage for either strategy. Also illustrates why study design is important, as 5' biased sequencing might likely cover these sites. ...
written 6 weeks ago by Collin850
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Comment: C: Variant Calling scRNA-seq data for KRAS mutations
... If this is cancer, most KRAS mutations (~80-90% of KRAS mutant tumors) occur at just one of two amino acids residues within the protein (G12X or G13X, X=any amino acid). So it would be entirely possible to have a manual component. ...
written 6 weeks ago by Collin850
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Comment: C: Get clinVar info for SNP with VEP
... My experience is similar in that disk speed can limit the speed of annotation. If you have a machine with a SSD you'll definitely get a speed boost. See the wiki for more detail: https://github.com/KarchinLab/open-cravat/wiki#system-capabilities . ...
written 5 months ago by Collin850
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Comment: C: Get clinVar info for SNP with VEP
... At least in my hands your first variant is generating a synonymous variant (BRAF D638D), which is not the same thing as the listed pathogenic variant. ...
written 5 months ago by Collin850
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Answer: C: Get clinVar info for SNP with VEP
... A lot of variants will likely produce an empty ClinVar field because ClinVar pathogenicity assertions are only available for a small number of variants. However, you could cross reference annotations with another variant annotator just to be sure. For example in [OpenCRAVAT][1], you could submit dir ...
written 5 months ago by Collin850
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Comment: C: Variant effect prediction
... A little clarification might help. Are you trying to predict whether variants are functionally damaging to proteins or are pathogenic (i.e. disease related)? Also, you mention a genome, are you also trying to prioritize non-coding variants? ...
written 5 months ago by Collin850
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Comment: C: How to go from VCF file to protein level
... Another potential alternative is [OpenCravat][1] [1]: https://opencravat.org/ ...
written 6 months ago by Collin850
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Comment: C: Mutation clustering in protein domains
... A word of caution about visual confirmation is that mutations can preferentially occur at certain nucleotide sequence contexts (e.g. CpG) which are not necessarily evenly distributed across the CDS of a protein. ...
written 7 months ago by Collin850
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Comment: C: How to download passenger mutations for cancer
... In CHASMplus, I used somatic mutations calls from the TCGA MC3 effort (pmid: 29596782), which provided a completely standardized way of mutation calling. Their pipeline was automated, so there likely are incorrect variant calls, but at least the data is consistent across many tumors. Another "gotch ...
written 7 months ago by Collin850
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Comment: C: How to download passenger mutations for cancer
... There are only one to several driver mutations per tumor, so the task of identifying driver mutations is your classical "needle in the haystack" problem. In my case, since I was using random forest, the under sampling was done through the bagging procedure of the random forest (randomForest R packag ...
written 7 months ago by Collin850

Latest awards to Collin

Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Difficulty replicating likelihood ratio test from RNA-seq paper
Appreciated 4 months ago, created a post with more than 5 votes. For A: BRCA1 and BRCA2 database's for NGS diagnostics purposes
Scholar 7 months ago, created an answer that has been accepted. For A: COSMIC data and rare variant
Scholar 8 months ago, created an answer that has been accepted. For A: COSMIC data and rare variant
Scholar 8 months ago, created an answer that has been accepted. For A: COSMIC data and rare variant
Appreciated 23 months ago, created a post with more than 5 votes. For A: BRCA1 and BRCA2 database's for NGS diagnostics purposes
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: Difficulty replicating likelihood ratio test from RNA-seq paper
Commentator 2.1 years ago, created a comment with at least 3 up-votes. For C: ROC curve for biomarkers
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Are there recommended steps if MuSiC reports too many significantly mutated genes
Commentator 2.7 years ago, created a comment with at least 3 up-votes. For C: ROC curve for biomarkers
Supporter 2.7 years ago, voted at least 25 times.
Appreciated 3.1 years ago, created a post with more than 5 votes. For A: BRCA1 and BRCA2 database's for NGS diagnostics purposes
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: Difficulty replicating likelihood ratio test from RNA-seq paper
Commentator 4.0 years ago, created a comment with at least 3 up-votes. For C: ROC curve for biomarkers
Popular Question 4.0 years ago, created a question with more than 1,000 views. For CRAVAT: a web tool to annotate and analyze cancer variants
Scholar 4.6 years ago, created an answer that has been accepted. For A: COSMIC data and rare variant
Teacher 4.6 years ago, created an answer with at least 3 up-votes. For A: Difficulty replicating likelihood ratio test from RNA-seq paper
Student 4.6 years ago, asked a question with at least 3 up-votes. For Are there recommended steps if MuSiC reports too many significantly mutated genes
Scholar 4.6 years ago, created an answer that has been accepted. For A: COSMIC data and rare variant

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