User: Vivek

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Vivek1.6k
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Bioinformatics Developer

Posts by Vivek

<prev • 209 results • page 1 of 21 • next >
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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 7 weeks ago by Vivek1.6k
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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 10 weeks ago by Vivek1.6k
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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 11 weeks ago by Vivek1.6k
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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 12 weeks ago by Vivek1.6k
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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 12 weeks ago by Vivek1.6k
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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 12 weeks ago by Vivek1.6k
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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 3 months ago by Vivek1.6k
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Answer: A: how to analyse gene expression using RNA-seq data
... You could visit a few RNA seq tutorials. They are by far the easiest to find in bioinformatics. Alternatively you can read through the manuals for the cufflinks suite. http://cole-trapnell-lab.github.io/cufflinks/manual/ The basic workflow is Reads -> Mapping to genome (STAR/Tophat etc are good ...
written 3 months ago by Vivek1.6k
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Answer: A: SVM based Filtering For NGS data
... As far as I'm aware, the only ML based software tool for variant filtering is the GATK's variant quality score recalibration and it uses a Gaussian mixture model. http://gatkforums.broadinstitute.org/gatk/discussion/39/variant-quality-score-recalibration-vqsr ...
written 3 months ago by Vivek1.6k
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Comment: C: Mapping two WGS Data
... You still need a reference genome to align using Magic Blast, which you do not have if you are comparing two sets of sequencing reads against each other. If I were you, I'd assemble the reads using SOAPdenovo and then align the resulting assemblies using BLAT. ...
written 3 months ago by Vivek1.6k

Latest awards to Vivek

Popular Question 5 weeks ago, created a question with more than 1,000 views. For 1000 Genomes and ESP Populations in Exome Aggregation Consortium Data
Appreciated 8 weeks ago, created a post with more than 5 votes. For A: Phasing trios for identification of denovo variants
Scholar 12 weeks ago, created an answer that has been accepted. For A: Identify overlapping coordinates
Scholar 3 months ago, created an answer that has been accepted. For A: Identify overlapping coordinates
Appreciated 5 months ago, created a post with more than 5 votes. For A: Phasing trios for identification of denovo variants
Scholar 5 months ago, created an answer that has been accepted. For A: Identify overlapping coordinates
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Identify overlapping coordinates
Scholar 7 months ago, created an answer that has been accepted. For A: Identify overlapping coordinates
Appreciated 10 months ago, created a post with more than 5 votes. For A: VCF files: Change Chromosome Notation
Popular Question 11 months ago, created a question with more than 1,000 views. For Variant Present In 1000 Genomes Data But Not In Esp
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Identify overlapping coordinates
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Identify overlapping coordinates
Popular Question 15 months ago, created a question with more than 1,000 views. For Vep Not Giving Annotation With Refseq Transcript
Popular Question 15 months ago, created a question with more than 1,000 views. For ClinVar download sources
Popular Question 17 months ago, created a question with more than 1,000 views. For Vep Not Giving Annotation With Refseq Transcript
Student 20 months ago, asked a question with at least 3 up-votes. For Identifying De Novo Variants In Trio Data
Scholar 22 months ago, created an answer that has been accepted. For A: Identify overlapping coordinates
Popular Question 23 months ago, created a question with more than 1,000 views. For Tabix Perl Api Examples
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: Identify overlapping coordinates
Popular Question 23 months ago, created a question with more than 1,000 views. For Cnvnator Run Time
Guru 2.4 years ago, received more than 100 upvotes.
Scholar 2.4 years ago, created an answer that has been accepted. For A: Identify overlapping coordinates
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Identify overlapping coordinates
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: Identify overlapping coordinates
Scholar 2.6 years ago, created an answer that has been accepted. For A: Identify overlapping coordinates

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