User: Kasthuri

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Kasthuri230
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230
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United States
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4 weeks ago
Joined:
7 years, 9 months ago
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k*******@gmail.com

Posts by Kasthuri

<prev • 48 results • page 1 of 5 • next >
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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 6 weeks 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 6 weeks ago by Kasthuri230 • updated 6 weeks ago by Kevin Blighe24k
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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 12 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 12 months ago by Kasthuri230
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Comment: C: ATAC data analysis
... Yes, that is one reasonable approach... ...
written 12 months ago by Kasthuri230
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Answer: A: ATAC data analysis
... Typically we use *diffbind* to find differentially binding sites between the control (closed chromatin) and experiment (open chromatin). I don't use Homer. But one can use *bedtools getfasta* to get the fasta sequences for those open chromatin peak sites and use *MEME* to get the consensus motif if ...
written 12 months ago by Kasthuri230
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sciClone + clonEvol on WES
... I have WES data for 3-time points - germline, diagnosis, and relapse. I can call "somatic" mutations between germline & diagnosis and diagnosis & relapse, that will enable me to do two time-point analysis using sciClone and clonEvol. However, I can call just SNPs in each of these time points ...
clonality analysis written 12 months ago by Kasthuri230 • updated 12 months ago by Samuel Brady230
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Comment: C: .clc to fastq
... Thanks genomax. I think the effort would be that the core would have to dig into the data in order to retrieve it. My collaborator didn't get the fastq file from the computational biologist who processed it and left the job. It is a matter of retracing the data. Anyway, if that needs to be done, he ...
written 14 months ago by Kasthuri230
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.clc to fastq
... My collaborator has processed .clc RNA seq data but not the fastq file which needs to be submitted to GEO. He needs to ask the core to get back the raw data, which requires considerable effort. Is there any repository that will accept .clc data? Alternatively, if anyone can recommend how to get back ...
rna-seq clc work bench written 14 months ago by Kasthuri230
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Comment: C: Do I have to realign from scratch?
... Yes, it is indeed hs37d5. Thank you so much, everyone! ...
written 15 months ago by Kasthuri230

Latest awards to Kasthuri

Popular Question 12 months ago, created a question with more than 1,000 views. For KeyError in MACS2
Epic Question 12 months ago, created a question with more than 10,000 views. For Vcf To Maf (Mutation Annotation Format) Conversion ?
Popular Question 13 months ago, created a question with more than 1,000 views. For Identifying germline and tumor samples
Appreciated 14 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 14 months ago, created a question with more than 5,000 views. For Vcf To Maf (Mutation Annotation Format) Conversion ?
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Whole Exome From Whole Genome
Student 2.3 years ago, asked a question with at least 3 up-votes. For Whole Exome From Whole Genome
Popular Question 3.8 years ago, created a question with more than 1,000 views. For Whole Exome From Whole Genome
Great Question 3.8 years ago, created a question with more than 5,000 views. For Vcf To Maf (Mutation Annotation Format) Conversion ?
Popular Question 3.8 years ago, created a question with more than 1,000 views. For Vcf To Maf (Mutation Annotation Format) Conversion ?
Popular Question 3.8 years ago, created a question with more than 1,000 views. For Chip-Seq Txt Data Into Sam Format.
Popular Question 3.8 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 Vcf To Maf (Mutation Annotation Format) Conversion ?
Student 5.4 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 6.5 years ago, asked a question with at least 3 up-votes. For Whole Exome From Whole Genome
Popular Question 6.5 years ago, created a question with more than 1,000 views. For Vcf To Maf (Mutation Annotation Format) Conversion ?

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