User: Naga

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Naga450
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Germany
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Posts by Naga

<prev • 23 results • page 1 of 3 • next >
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Comment: C: Somatic Mutation Identification without Paired Normal Sample
... You should create a small pipeline to perform this. To make it simple, 1. download the non-TCGA ExAC data set from the [ftp][1]. 2. Use tabix to get AF for each of the variant in your no-control sample against ExAC vcf file. 3. Remove the common variants [1]: ftp://ftp.broadinstitute.org/p ...
written 2.3 years ago by Naga450
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Answer: A: Somatic Mutation Identification without Paired Normal Sample
... You can still use them, as you mentioned create a local control from the 90 samples, and also use ExAC to remove the common variants (with MAF > 0.01%). The remaining will be the somatic and rare germline variants. In Exome, you will have at least 100-200 germline functional variants with this MA ...
written 2.3 years ago by Naga450
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Comment: C: Heatmaps in R
... And also ComplexHeatmap https://bioconductor.org/packages/release/bioc/html/ComplexHeatmap.html ...
written 2.6 years ago by Naga450
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Answer: A: VCF file with AF(allele frequency)
... If you are looking for frequency of variants in the population, i.e., Minor allele frequency (MAF), annotate the variants with 1000 genome data or ExAC. And if you are looking for variant allele frequency (VAF), to determine, whether it is heterozygous or homozygous, use DP4 field.  DP4 is Number ...
written 3.7 years ago by Naga450
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Comment: C: How To Determine If A Given Species Or Taxon Id Corresponds To A Pathogen Or Not
... Seems summary table have been moved to a different folder. https://twitter.com/ncbi/status/177844734147039232. ftp://ftp.ncbi.nih.gov/genomes/GENOME_REPORTS/ But these txt files doesn't have the "pathogen in" column. It is also not listed here in http://www.ncbi.nlm.nih.gov/genome/browse/ As sugges ...
written 4.1 years ago by Naga450
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Answer: A: frequently found false positives from exome seq
... It is danger to filter out these genes (as stated in the blog). But you can create a blacklist of variants from your in-house exome data, sequenced for other projects/phenotype/families. And remove the variants that appear in both dataset. This will reduce FP, but does not remove all of them. Then ...
written 4.6 years ago by Naga450
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Comment: C: Variant Function Prediction
... GRCh37 and h19 are same. So, PROVEAN should work. ...
written 5.0 years ago by Naga450
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Answer: A: Variant Function Prediction
... You can also use MutationTaster and Provean ...
written 5.0 years ago by Naga450
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Comment: C: Output Of Running Hhblits With Multithread
... I think this causes your error "/home/chris/Bioinformatics/results/Mimi/$name.a3m", try "$name.a3m" instead ...
written 5.6 years ago by Naga450
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Comment: C: Database For Protein Expression?
... Correct usage: 'Protein synthesis' and 'Gene expression' ...
written 5.6 years ago by Naga450

Latest awards to Naga

Appreciated 23 months ago, created a post with more than 5 votes. For A: [Fastacmd] How To Retrieve Sequence From Blast Db
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Calculating The Performance Of A Tool
Supporter 4.9 years ago, voted at least 25 times.
Voter 4.9 years ago, voted more than 100 times.
Good Answer 7.4 years ago, created an answer that was upvoted at least 5 times. For A: Complete Protein Structure When Only Alpha Carbons Are Known
Appreciated 7.4 years ago, created a post with more than 5 votes. For A: Complete Protein Structure When Only Alpha Carbons Are Known
Teacher 7.4 years ago, created an answer with at least 3 up-votes. For A: Complete Protein Structure When Only Alpha Carbons Are Known
Teacher 7.5 years ago, created an answer with at least 3 up-votes. For A: [Fastacmd] How To Retrieve Sequence From Blast Db
Teacher 7.6 years ago, created an answer with at least 3 up-votes. For A: How To Determine If A Given Species Or Taxon Id Corresponds To A Pathogen Or Not
Good Answer 7.6 years ago, created an answer that was upvoted at least 5 times. For A: How To Determine If A Given Species Or Taxon Id Corresponds To A Pathogen Or Not
Commentator 7.6 years ago, created a comment with at least 3 up-votes. For C: Automatically Getting The Ncbi Taxonomy Id From The Genbank Identifier
Student 7.7 years ago, asked a question with at least 3 up-votes. For Calculating The Performance Of A Tool
Teacher 7.8 years ago, created an answer with at least 3 up-votes. For A: Classsify Species Into Groups

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