User: subhajit06

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subhajit06110
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United States
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2 years, 11 months ago
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6 years, 6 months ago
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Posts by subhajit06

<prev • 10 results • page 1 of 1 • next >
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Answer: A: DNA-seq and RNA-seq bam from TCGA for a single sample
... Thank you !! I will try that and let you know. Thanks for your helpful comment ! ...
written 3.0 years ago by subhajit06110
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Answer: A: DNA-seq and RNA-seq bam from TCGA for a single sample
... Thanks for your answer. We do have controlled data access. I am using GDC with the token to get level 1/2 data. I wanna know, if anyone knows about a good data set (a set of samples) with both DNA-seq and RNA-seq bam files and vcf file with snv call. ...
written 3.0 years ago by subhajit06110
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DNA-seq and RNA-seq bam from TCGA for a single sample
... Hello all, I am trying to find DNA-seq bam file and RNA-seq bam file from one sample. I also need vcf file for SNV callset. I am looking for some examples from TCGA data. It would be great if anyone could point out a paper that use dataset of this kind. Thanks for your help, --Subhajit ...
dna-seq one sample rna-seq bam written 3.0 years ago by subhajit06110
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Comment: C: How to run ABSOLUTE with WGS bam files ?
... Hi Chris, Thanks for your reply. Does copyCat handle WXS data ?? ...
written 4.3 years ago by subhajit06110
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Comment: C: How to run ABSOLUTE with WGS bam files ?
... Thanks Yunku for your help and Sorry for my late reply. ...
written 4.3 years ago by subhajit06110
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Mismatch in exome capture and mapping reference assembly in TCGA WXS data ?
... Hi all, I have one question. We wanted to call Copy number for some of TCGA WXS samples. But we noticed that the exome capture kit (target bed file) that was used, was based on hg18 (more specifically is was hg18 nimblegen exome version 2). In fact we went and verified that this bed file coordina ...
whole exome data tcga exome capture file cnv call written 4.3 years ago by subhajit06110 • updated 4.3 years ago by Cyriac Kandoth5.5k
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How to run ABSOLUTE with WGS bam files ?
... Dear all, I have a question regarding Copy Number analysis using ABSOLUTE software from Broad Institute. I want to call CNA for a Tumor with matched Normal and I have both Tumor and Normal bam files. I have installed ABSOLUTE but I am not sure how to use it for NGS data. I think the example that ...
absolute next-gen matched normal tumor bam file written 4.4 years ago by subhajit06110 • updated 7 months ago by roseluosy0
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Comment: C: CNV analysis tool on exome data for NGS
... Thanks Irsan for your detailed answer. Let me figure out all the subparts of your answer :) as I am kind of learning these all tools these days. ...
written 6.5 years ago by subhajit06110
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Comment: A: CNV analysis tool on exome data for NGS
... Hi Hersman, Jorge and Fred .. thanks for your comments. I will try to play around with those softwares you guyz mentioned. ...
written 6.5 years ago by subhajit06110 • updated 10 months ago by RamRS30k
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CNV analysis tool on exome data for NGS
... Dear all, I have a question regarding Copy Number analysis on Exome sequencing data.(NGS data)   I have multiple BAM files (around 30) and I have some target regions which I want to check if there is any Copy number gain. What would be the best way to do it? I am a newbie in this field and it see ...
exome next-gen cnv bam written 6.5 years ago by subhajit06110 • updated 6.1 years ago by Christian2.9k

Latest awards to subhajit06

Great Question 4.4 years ago, created a question with more than 5,000 views. For CNV analysis tool on exome data for NGS
Appreciated 6.3 years ago, created a post with more than 5 votes. For CNV analysis tool on exome data for NGS
Prophet 6.3 years ago, created a post with more than 20 followers. For CNV analysis tool on exome data for NGS
Good Question 6.3 years ago, asked a question that was upvoted at least 5 times. For CNV analysis tool on exome data for NGS
Popular Question 6.3 years ago, created a question with more than 1,000 views. For CNV analysis tool on exome data for NGS
Student 6.5 years ago, asked a question with at least 3 up-votes. For CNV analysis tool on exome data for NGS

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