User: prashant10991

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Posts by prashant10991

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Accessing population specific mutation data from 1000 genome.
... I am trying to download mutation data from 1000 genome. I am interested in white/not Hispanic or Latino population for the study. I have a few questions regarding the data. 1. From the mentioned category on the 1000 genome (http://www.internationalgenome.org/faq/which-populations-are-part-your-stud ...
vcf 1000gnome mutation written 7 days ago by prashant109910 • updated 5 days ago by Kevin Blighe37k
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Comment: C: Too many distinct mutations in matched normal and cancer cells
... Data is not publically available. It can be downloaded by requesting here http://txcrb.org/data.html. This same link is also present in the article I mentioned above along with all the preprocessing. I am using the filtered VCF files shared by the authors. However I see no issue in sharing a snippe ...
written 10 days ago by prashant109910 • updated 10 days ago by finswimmer10k
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Too many distinct mutations in matched normal and cancer cells
... Hi, I am working on the exome sequencing data shared by https://www.nature.com/articles/sdata201610. To summarize the dataset, they sequenced exomes of cancer tissues and blood cells as matched normal of 7 different patients. I have acquired VCF files of 3 patients with the same type of cancers. ...
vcf exome snp cancer written 10 days ago by prashant109910
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Comment: C: Genome Assembly vs Reference Genome for slicing around mutation location.
... Specifically, I am trying to learn the distributed representation of variants using some similar strategy to word2vec. So I want to slice DNA of 2*K+1 length centered around a mutation. But, I am in a dilemma of what is the correct way to slice the DNA so that most of the information is preserved. ...
written 28 days ago by prashant109910
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Genome Assembly vs Reference Genome for slicing around mutation location.
... I have a bam file and corresponding vcf file from some source. I am trying to slice the DNA across its mutation location to feed into one of the algorithms. I wanted to know what is the right way to do this. I have two options 1. I can create a genome assembly/contigs from the bam file and then sl ...
genome assembly mutation rna-seq written 29 days ago by prashant109910

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