User: Kasthuri

gravatar for Kasthuri
Kasthuri220
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220
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United States
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2 months, 1 week ago
Joined:
6 years, 11 months ago
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k*******@gmail.com

Posts by Kasthuri

<prev • 46 results • page 1 of 5 • next >
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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 10 weeks ago by Kasthuri220
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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 10 weeks ago by Kasthuri220
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Comment: C: ATAC data analysis
... Yes, that is one reasonable approach... ...
written 10 weeks ago by Kasthuri220
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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 10 weeks ago by Kasthuri220
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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 10 weeks ago by Kasthuri220 • updated 10 weeks 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 3 months ago by Kasthuri220
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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 3 months ago by Kasthuri220
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Comment: C: Do I have to realign from scratch?
... Yes, it is indeed hs37d5. Thank you so much, everyone! ...
written 4 months ago by Kasthuri220
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Do I have to realign from scratch?
... I am working with human genomes I downloaded from TCGA (all bam files). I wanted to run GATK DepthOfCoverage which complained that the contigs are not compatible. I think GATK recommends aligning from scratch. Is there an easier way around than aligning from scratch? I tried Picard's ReorderSam but ...
gatk incompatible contigs written 4 months ago by Kasthuri220 • updated 4 months ago by genomax33k
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Comment: C: Allele frequency of a gene from a .bam file.
... Thank you Pierre. Yes, I get that we can get AF from variants. But I am looking at some metric for a region, in general, like beta allele frequency they compute when calling CNVs. ...
written 5 months ago by Kasthuri220

Latest awards to Kasthuri

Popular Question 3 months ago, created a question with more than 1,000 views. For Identifying germline and tumor samples
Appreciated 4 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 4 months ago, created a question with more than 5,000 views. For Vcf To Maf (Mutation Annotation Format) Conversion ?
Popular Question 17 months ago, created a question with more than 1,000 views. For Whole Exome From Whole Genome
Student 17 months ago, asked a question with at least 3 up-votes. For Whole Exome From Whole Genome
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Vcf To Maf (Mutation Annotation Format) Conversion ?
Great Question 2.9 years ago, created a question with more than 5,000 views. For Vcf To Maf (Mutation Annotation Format) Conversion ?
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Whole Exome From Whole Genome
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Chip-Seq Txt Data Into Sam Format.
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Vcf To Maf (Mutation Annotation Format) Conversion ?
Popular Question 3.3 years ago, created a question with more than 1,000 views. For Vcf To Maf (Mutation Annotation Format) Conversion ?
Student 4.6 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 5.7 years ago, asked a question with at least 3 up-votes. For Whole Exome From Whole Genome
Popular Question 5.7 years ago, created a question with more than 1,000 views. For Vcf To Maf (Mutation Annotation Format) Conversion ?

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