User: Kasthuri

gravatar for Kasthuri
Kasthuri230
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Posts by Kasthuri

<prev • 53 results • page 1 of 6 • next >
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Comment: C: Does mitotic activity inversely correlate with HiC interactions data?
... Thanks! Yes, I realized the HiC interactions are mapped during interphase. This is my exact question: Let's say I capture some cells and do a HiC on it. If none of the cells is undergoing mitosis, and all of them have passed the mitotic stage, are the interactions reflective of underlying cell densi ...
written 9 weeks ago by Kasthuri230
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Does mitotic activity inversely correlate with HiC interactions data?
... At least at the outset, it appears if the interchromosomal interactions are higher as determined by HiC then we might expect lower mitotic activity and vice-versa. Can anyone confirm this or suggest relevant literature that validates/invalidates this hypothesis? Thanks! ...
next-gen written 9 weeks ago by Kasthuri230 • updated 9 weeks ago by Jean-Karim Heriche16k
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Comment: C: Expanding bed format into single nucleotide resolution
... Awesome! Thank you very much. ...
written 10 weeks ago by Kasthuri230
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Expanding bed format into single nucleotide resolution
... I have a TCGA CNV data: chrom loc.start loc.end num.mark seg.mean 1 3218610 3586250 166 0.1112 which I would like to expand as: chrom loc.start seg.mean 1 3218610 0.1112 1 3218611 0.1112 1 3218612 0.1112 ... ...
genome written 10 weeks ago by Kasthuri230 • updated 10 weeks ago by Alex Reynolds26k
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Whole exomes - More than 3 time points
... Hi, I am trying to infer clonality in cancers and I am wondering if there are any studies that have done WES for more than three time points for each patient. Thanks, Kasthuri ...
next-gen written 3 months ago by Kasthuri230
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Comment: C: TCGA Copy Number Data in Rdata format
... Thanks Kevin. Actually I am working with pancreas TCGA and could see several other cancers except that. It will be great if I could have that. Best K. ...
written 5 months ago by Kasthuri230
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TCGA Copy Number Data in Rdata format
... Hi, I am working with clonality analysis software in which one of the arguments is seg.mat.loc="tcga.blca.seg.hg19.rdata" It is segmented TCGA copy number data but in R format. The package is not so clear in explaining where it could be found. Here is the package info: https://bitbucket.org/nmcg ...
tcga copy number r format written 5 months ago by Kasthuri230 • updated 5 months ago by Kevin Blighe32k
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Comment: C: sciClone + clonEvol on WES
... Thanks! I did that. I was trying to get some cool fishplots - thinking that increasing the time points will give me better ones. But unfortunately, not :-( ...
written 16 months ago by Kasthuri230
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Comment: C: ATAC data analysis
... You need to have a bed file - just use the chromosome, start and end position and get the fasta sequences through bedtools and use MEME. ...
written 16 months ago by Kasthuri230
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Comment: C: ATAC data analysis
... Yes, that is one reasonable approach... ...
written 16 months ago by Kasthuri230

Latest awards to Kasthuri

Popular Question 16 months ago, created a question with more than 1,000 views. For KeyError in MACS2
Epic Question 16 months ago, created a question with more than 10,000 views. For Vcf To Maf (Mutation Annotation Format) Conversion ?
Popular Question 17 months ago, created a question with more than 1,000 views. For Identifying germline and tumor samples
Appreciated 18 months ago, created a post with more than 5 votes. For How To Visually Display What Protein Domains Are Affected By A Mutation
Great Question 18 months ago, created a question with more than 5,000 views. For Vcf To Maf (Mutation Annotation Format) Conversion ?
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Whole Exome From Whole Genome
Student 2.6 years ago, asked a question with at least 3 up-votes. For Whole Exome From Whole Genome
Popular Question 4.1 years ago, created a question with more than 1,000 views. For Whole Exome From Whole Genome
Great Question 4.1 years ago, created a question with more than 5,000 views. For Vcf To Maf (Mutation Annotation Format) Conversion ?
Popular Question 4.1 years ago, created a question with more than 1,000 views. For Vcf To Maf (Mutation Annotation Format) Conversion ?
Popular Question 4.1 years ago, created a question with more than 1,000 views. For Chip-Seq Txt Data Into Sam Format.
Popular Question 4.1 years ago, created a question with more than 1,000 views. For Vcf To Maf (Mutation Annotation Format) Conversion ?
Popular Question 4.4 years ago, created a question with more than 1,000 views. For Vcf To Maf (Mutation Annotation Format) Conversion ?
Student 5.7 years ago, asked a question with at least 3 up-votes. For How To Visually Display What Protein Domains Are Affected By A Mutation
Student 6.8 years ago, asked a question with at least 3 up-votes. For Whole Exome From Whole Genome
Popular Question 6.8 years ago, created a question with more than 1,000 views. For Vcf To Maf (Mutation Annotation Format) Conversion ?

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