User: Vivek

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Vivek1.7k
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Bioinformatics Developer

Posts by Vivek

<prev • 212 results • page 1 of 22 • next >
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Comment: C: tips for checking variants in IGV
... Defaults should be fine, I never experimented with those. You'll be doing manual inspection anyways. ...
written 2 days ago by Vivek1.7k
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Answer: A: tips for checking variants in IGV
... Some things I look at: 1. Base qualities at the locus and mapping qualities of the reads supporting the variant 2. Frequency of mutations or INDELs within 1 KB region on either side 3. Allele fraction on both strands ...
written 2 days ago by Vivek1.7k
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Answer: A: question regarding bioinformatics jobs in US
... PIs usually don't consider hiring someone as a Bioinformatician with no prior experience or relevant education, its a high pressure job around deadlines where the learning curve is pretty steep even for well trained people. However some larger genome centers have entry level QC positions available ...
written 3 days ago by Vivek1.7k
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Calculating minor allele concordance
... Hi, I have performed an imputation on genotyped data for around 100k individuals, since we also happen to have exome sequencing for a subset of these people on which I have done variant calling, I wanted to use this as a QC measure to evaluate the accuracy of my imputation. However when you calcul ...
maf array exome impute concordance written 12 weeks ago by Vivek1.7k
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Answer: A: Protein Change Annotation from Oncotator
... What file format are you supplying to oncotator? If its VCF, all the variants are assumed to be on the positive strand. ...
written 3 months ago by Vivek1.7k
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Answer: A: About Bioinformatics PhD programs
... The ranking depends less on school name and far more on the PI and the lab you are going to be working with. ...
written 3 months ago by Vivek1.7k
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Answer: A: Question about GATK hardfiltering conditions
... That GATK filtering expression is not for the variants that PASS, you are writing that expression for the variants that FAIL. Whatever remains is tagged as PASS. ...
written 3 months ago by Vivek1.7k
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Answer: A: Principal Component Analysis
... I think you are describing the Oxford gen/sample format here. You can use something like qctool or gtool to convert them to PLINK binary format and use the standard PCA tools. ...
written 3 months ago by Vivek1.7k
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Answer: A: plot coverage for WES data
... Simplest way would be to just extract chr1 from all BAM files and view them with IGV. ...
written 4 months ago by Vivek1.7k
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Comment: C: how to analyse gene expression using RNA-seq data
... In guided transcriptome assembly you give the assembler a GTF file of known transcripts/isoforms for the organism you are interested in to aid as a guiding reference. In unguided assembly, you don't which can lead the assembler into assembling more de novo isoforms, if that is your objective. ...
written 4 months ago by Vivek1.7k

Latest awards to Vivek

Teacher 3 days ago, created an answer with at least 3 up-votes. For A: Identify overlapping coordinates
Popular Question 10 weeks ago, created a question with more than 1,000 views. For 1000 Genomes and ESP Populations in Exome Aggregation Consortium Data
Appreciated 3 months ago, created a post with more than 5 votes. For A: Phasing trios for identification of denovo variants
Scholar 3 months ago, created an answer that has been accepted. For A: Identify overlapping coordinates
Scholar 4 months ago, created an answer that has been accepted. For A: Identify overlapping coordinates
Appreciated 6 months ago, created a post with more than 5 votes. For A: Phasing trios for identification of denovo variants
Scholar 6 months ago, created an answer that has been accepted. For A: Identify overlapping coordinates
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Identify overlapping coordinates
Scholar 8 months ago, created an answer that has been accepted. For A: Identify overlapping coordinates
Appreciated 11 months ago, created a post with more than 5 votes. For A: VCF files: Change Chromosome Notation
Popular Question 12 months ago, created a question with more than 1,000 views. For Variant Present In 1000 Genomes Data But Not In Esp
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Identify overlapping coordinates
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Identify overlapping coordinates
Popular Question 16 months ago, created a question with more than 1,000 views. For Vep Not Giving Annotation With Refseq Transcript
Popular Question 16 months ago, created a question with more than 1,000 views. For ClinVar download sources
Popular Question 18 months ago, created a question with more than 1,000 views. For Vep Not Giving Annotation With Refseq Transcript
Student 21 months ago, asked a question with at least 3 up-votes. For Identifying De Novo Variants In Trio Data
Scholar 23 months ago, created an answer that has been accepted. For A: Identify overlapping coordinates
Popular Question 24 months ago, created a question with more than 1,000 views. For Tabix Perl Api Examples
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: Identify overlapping coordinates
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Scholar 2.5 years ago, created an answer that has been accepted. For A: Identify overlapping coordinates
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: Identify overlapping coordinates
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: Identify overlapping coordinates

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