User: Prateek
Prateek • 1000
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Bioinformatics Engineer
Posts by Prateek
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... Hi
Does COSMIC database has ploidy information for samples / variants in their database? Can anyone suggest a way to obtain that?
Thanks
...
written 4.8 years ago by
Prateek • 1000
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... 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 6.3 years ago by
Prateek • 1000
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... 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 6.7 years ago by
Prateek • 1000
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... 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 ...
written 6.7 years ago by
Prateek • 1000
1
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... 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 6.8 years ago by
Prateek • 1000
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... @Michael - clustering can be done on 1-d data too, but yes - not sure what biological question it serves in this case. ...
written 6.8 years ago by
Prateek • 1000
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... 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 6.8 years ago by
Prateek • 1000
63
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31 follow
8
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... 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 ...
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Comment:
C: Predicted Impact Of Indels?
... nice alternative to ANNOVAR ...
written 7.3 years ago by
Prateek • 1000
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... @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 7.4 years ago by
Prateek • 1000
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For What Are The 'Copy Number Detection' Tools Out There For Exome Capture Ngs Data.
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For How Many Is Too Many? Germline And Somatic Coding Indels And Snps In Cancer Exome Capture.
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For A: Getting Watson Snps From Biomart
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