User: Prateek

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Prateek990
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Boston, MA
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3 years, 10 months ago
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Bioinformatics Engineer

Posts by Prateek

<prev • 54 results • page 1 of 6 • next >
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Ploidy Information For Cosmic Samples/Variants
... Hi Does COSMIC database has ploidy information for samples / variants in their database? Can anyone suggest a way to obtain that? Thanks ...
written 3.8 years ago by Prateek990
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Answer: A: What Is The Best Strategy To Find Gwas Data Based On Certain Keywords
... See NextBio: http://www.nextbio.com - use their curated studies tab at the top and enter your search query. You can apply filters / check attributes like GWAS studies etc. using advanced option - or you can download all and then manually select those directly relevant. for example, prostate cancer y ...
written 5.3 years ago by Prateek990
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Answer: A: Sources Of Publicly Available Human Whole Genome Sequence Data
... TCGA hosts canacer sequencing data: https://tcga-data.nci.nih.gov/tcga/ COSMIC again is a database of cancer mutations but also includes those identified as germline mutations: http://www.sanger.ac.uk/genetics/CGP/cosmic/biomart/martview/ ...
written 5.7 years ago by Prateek990
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How To Set Attribute As Checked By Default In Biomart 0.8
... I am trying to configure a portal using biomart 0.8 release and want to set some attributes as checked by default in the interface (for example, the way in which ensembl biomart has transcript ID , gene ID already checked in attributes->features). martconfigurator (portal view) has a "default" p ...
biomart written 5.7 years ago by Prateek990
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Answer: A: Open Source Ngs Variant Database.
... This paper describes Ensembl's variation schema and API. http://www.biomedcentral.com/1471-2105/11/238 You could also set up a local version of ensembl biomart's variation database and use its API to populate it with your own variation data. ...
written 5.8 years ago by Prateek990
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Comment: C: Clustering Million Points : Transcript Start And End Sites
... @Michael - clustering can be done on 1-d data too, but yes - not sure what biological question it serves in this case. ...
written 5.8 years ago by Prateek990
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Comment: C: Is There A Lims That Doesn'T Suck?
... Great work Brad - I was wondering if you plan to add functionality for being able to create capture and capture pools from libraries to be transferred into individual lanes. Am I right that this is not there yet or did I miss it? ...
written 5.9 years ago by Prateek990
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What Are The 'Copy Number Detection' Tools Out There For Exome Capture Ngs Data.
... Do you know of any CNV detection tools for NGS paired-end exome data - coverage method (window based) or paired-end mapping method (clustering based)? I am aware its a tough problem to solve and have looked at some tools for whole genome but couldn't find one for exome. I would also welcome discus ...
next-gen copynumber variant sequencing cnv structural written 6.2 years ago by Prateek990 • updated 2.4 years ago by Biostar ♦♦ 20
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Comment: C: Predicted Impact Of Indels?
... nice alternative to ANNOVAR ...
written 6.3 years ago by Prateek990
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Comment: C: How Many Is Too Many? Germline And Somatic Coding Indels And Snps In Cancer Exom
... @Chris - you were right. A lot of them are from dbSNP. However, I still need to find out how and why so many of them can be tolerated in a single individual! ...
written 6.4 years ago by Prateek990

Latest awards to Prateek

Guru 3.8 years ago, received more than 100 upvotes.
Supporter 3.8 years ago, voted at least 25 times.
Good Question 6.2 years ago, asked a question that was upvoted at least 5 times. For What Are The 'Copy Number Detection' Tools Out There For Exome Capture Ngs Data.
Teacher 7.1 years ago, created an answer with at least 3 up-votes. For A: The Best Question To Ask In A Bioinformatics Seminar
Appreciated 7.1 years ago, created a post with more than 5 votes. For A: The Best Question To Ask In A Bioinformatics Seminar
Good Answer 7.1 years ago, created an answer that was upvoted at least 5 times. For A: The Best Question To Ask In A Bioinformatics Seminar
Popular Question 7.1 years ago, created a question with more than 1,000 views. For How To Obtain Chromosome Locus From Coordinates
Appreciated 7.1 years ago, created a post with more than 5 votes. For A: How To Run Clustalw Using Commands From An Input File
Good Answer 7.1 years ago, created an answer that was upvoted at least 5 times. For A: How To Run Clustalw Using Commands From An Input File
Teacher 7.1 years ago, created an answer with at least 3 up-votes. For A: How To Run Clustalw Using Commands From An Input File
Good Question 7.1 years ago, asked a question that was upvoted at least 5 times. For Algorithms Predicting Effects Of Snps / Aa Substitution On Protein
Student 7.1 years ago, asked a question with at least 3 up-votes. For Algorithms Predicting Effects Of Snps / Aa Substitution On Protein
Appreciated 7.1 years ago, created a post with more than 5 votes. For Algorithms Predicting Effects Of Snps / Aa Substitution On Protein
Popular Question 7.1 years ago, created a question with more than 1,000 views. For Algorithms Predicting Effects Of Snps / Aa Substitution On Protein
Student 7.1 years ago, asked a question with at least 3 up-votes. For What Is More Relevant In Bioinformatics: Databases Or Algorithms
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Teacher 7.1 years ago, created an answer with at least 3 up-votes. For A: Getting Watson Snps From Biomart

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