Moderator: Ashutosh Pandey

gravatar for Ashutosh Pandey
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Location:
Philadelphia
Website:
https://www.linkedin.c...
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Last seen:
1 month, 1 week ago
Joined:
5 years, 6 months ago
Email:
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I am a computational biologist at GlaxoSmithKline. My research interest focuses on using high-throughput genetic and genomic data to study the impact of genomic variation on gene expression and phenotypes.

Research Interests:

Computational Genomics
Next generation sequencing
Complex trait analysis
Information retrieval 

Posts by Ashutosh Pandey

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Comment: C: sequence in different line
... Substitute tab or space with newline use unix tr ...
written 3 months ago by Ashutosh Pandey11k
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Job: Host-Microbe Bioinformatics Post-Doctoral Fellow GlaxoSmithKline, Collegeville, Pennsylvania
... **Host-Microbe Bioinformatics Post-Doctoral Fellow GlaxoSmithKline, Collegeville, Pennsylvania** In GlaxoSmithKline R&D (http://www.gsk.com/research.html), computational biologists have a broad and essential role in drug discovery through the integrative analysis of internal and external biome ...
microbiome job postdoc written 13 months ago by Ashutosh Pandey11k
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Job: Computational Biologist, GlaxoSmithKline - King of Prussia, PA
... **Employment type** Full-time **Experience** Mid-Senior level **Job description** Details: The Computational Biology Department supports Drug Discovery and Development at GSK Pharmaceuticals R&D through the integrative analysis of internal and external biomedical data. Our analysis competenci ...
computational biologist job written 19 months ago by Ashutosh Pandey11k
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Job: Computational Biology Data Manager, GlaxoSmithKline - King of Prussia, PA
... **Employment type** Full-time **Experience** Mid-Senior level **Basic Qualifications** A first or an advanced degree (MS or PhD) in a life science, physical science, computational science or mathematics; or equivalent experience. A thorough understanding of linux and windows. Demonstrated skills ...
data manager computational biologist job written 19 months ago by Ashutosh Pandey11k
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Comment: C: Log transformation of RPKM data for PCA analysis
... Adding 1 is more suitable as log2 of values less than 1 will give negative values.    ...
written 2.1 years ago by Ashutosh Pandey11k
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Comment: C: Using phastCons30way in UCSC table browser
... Assuming that your genome of interest is 'Human' Go to Table Browser Select 1) genome as 'Human' 2) group as 'Comparative Genomics' 3) track as 'Conservation' 4) table as 'phastCons100way' 5) enter coordinates for your region of interest in position 6) Select the output format and click on get out ...
written 2.1 years ago by Ashutosh Pandey11k
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Comment: C: BWA and mapping
... It will have both reads for a pair irrespective of whether one of them remained unmapped or mapped at too many positions. The second column in the BAM file will be properly flagged as explained here: http://broadinstitute.github.io/picard/explain-flags.html ...
written 2.1 years ago by Ashutosh Pandey11k
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Answer: C: Replace vcf in-house variant IDs with dnSNP variant IDs
... If I understood your question GATK's VariantAnnotator may help you. It can take dbSNP vcf file and your vcf file as inputs and append dbSNP rsIDs to your vcf file. Below is the link: correctly https://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_walkers_annotator_VariantAnnotat ...
written 2.1 years ago by Ashutosh Pandey11k
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Comment: C: Conservation score for selected species
... The two resources I can think of now: 1) GERP++ scores: http://mendel.stanford.edu/SidowLab/downloads/gerp/ 2) PhastCons scores from UCSC: Here is a relevant post (https://www.biostars.org/p/16724/#16731) ...
written 2.1 years ago by Ashutosh Pandey11k
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Comment: C: Genotype (DNA-Seq) - Phenotype (RNA-Seq) database
... http://www.gtexportal.org/home/ Description: http://www.genome.gov/27543767 ...
written 2.1 years ago by Ashutosh Pandey11k

Latest awards to Ashutosh Pandey

Appreciated 3 months ago, created a post with more than 5 votes. For A: How to find the differences between filtered and unfiltered VCF files
Appreciated 3 months ago, created a post with more than 5 votes. For A: How to find the differences between filtered and unfiltered VCF files
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: hello i know i must accept that im a stupid
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Compare Vcf Files
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: What Are The Differences Between The Dna Sequences Of Two Alleles Of A Gene
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Good Question 11 months ago, asked a question that was upvoted at least 5 times. For Bam Header Edit
Good Answer 11 months ago, created an answer that was upvoted at least 5 times. For A: What Are The Differences Between The Dna Sequences Of Two Alleles Of A Gene
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Scholar 11 months ago, created an answer that has been accepted. For A: what is the properties of filtering the vcf files
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Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Picard Fixmate Necessaary
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Popular Question 11 months ago, created a question with more than 1,000 views. For Cufflinks And Solid 5500 Rnaseq Bam Files
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Appreciated 12 months ago, created a post with more than 5 votes. For A: Where To Download Mouse Mm10 Dbsnp Database With Vcf Format
Great Question 12 months ago, created a question with more than 5,000 views. For Vcf Format And Filtering
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