Moderator: Ashutosh Pandey
Ashutosh Pandey ♦ 11k
- Reputation:
- 10,960
- Status:
- Trusted
- Location:
- Philadelphia
- Website:
- https://www.linkedin.c...
- Scholar ID:
- Google Scholar Page
- Last seen:
- 1 month ago
- Joined:
- 6 years, 2 months ago
- Email:
- a***********@gmail.com
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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... I did my Masters and PhD from Memphis. Great place to be a student as cost of living is low. ...
written 5 months ago by
Ashutosh Pandey ♦ 11k
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Comment:
C: sequence in different line
... Substitute tab or space with newline use unix tr ...
written 11 months ago by
Ashutosh Pandey ♦ 11k
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... **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 ...
written 21 months ago by
Ashutosh Pandey ♦ 11k
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... **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 ...
written 2.3 years ago by
Ashutosh Pandey ♦ 11k
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... **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 ...
written 2.3 years ago by
Ashutosh Pandey ♦ 11k
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... Adding 1 is more suitable as log2 of values less than 1 will give negative values.
...
written 2.7 years ago by
Ashutosh Pandey ♦ 11k
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... 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 2.8 years ago by
Ashutosh Pandey ♦ 11k
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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 2.8 years ago by
Ashutosh Pandey ♦ 11k
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... 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 2.8 years ago by
Ashutosh Pandey ♦ 11k
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... 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 2.8 years ago by
Ashutosh Pandey ♦ 11k
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For Host-Microbe Bioinformatics Post-Doctoral Fellow GlaxoSmithKline, Collegeville, Pennsylvania
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For A: Samtools: Why Have I Been Using "View" Command For Mpileup
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