User: anjali.gopal91

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Posts by anjali.gopal91

<prev • 14 results • page 1 of 2 • next >
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For protein binding microarrays, how do you extract an 8mer sequence from your 35mer sequence?
... I'm having trouble finding papers that describe how to convert a 35mer sequence to the 8mer motif representative of a TF binding sequence (given a dataset of 35mer motifs and the mean signal intensity). If anyone has additional resources for this, would you be able to refer me to it? Thanks! ...
pbm chip-seq written 4.7 years ago by anjali.gopal9150
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Viral Genome SNP and Indel Detection
... Hi all, I'm trying to call snps and indels for HIV, and I'm wondering if there are suggestions for good mutation detection software for viruses. I expect to have fairly large indels (20-30bp in a 9kb genome), as well as the regular snps, across multiple  samples that are pooled together in one run. ...
alignment snp sequencing written 5.0 years ago by anjali.gopal9150 • updated 5.0 years ago by Brian Bushnell17k
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Can someone help me come up with a step-by-step algorithm for NGS CNV analysis?
... Problem: I want to analyze copy numbers for whole-genome next generation sequencing data, for non-human samples. Ideally, I'd copy number information displayed in something like the UCSC genome browser, which means I need copy number info for every point (e.g., assume window size of 1000) along the ...
ngs cnv written 5.4 years ago by anjali.gopal9150 • updated 5.4 years ago by Eric T.2.6k
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Comment: C: Sliding Window for CNV Analysis
... Thanks! This was really detailed and helpful. A followup question: suppose I used a 100bp window to calculate CNV, and I want to create a plot of CNV in chrI. With a static window, I can do this very easily, i.e., divide up the chromosome into 100bp regions, perform the calculations, and use the ou ...
written 5.5 years ago by anjali.gopal9150
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Sliding Window for CNV Analysis
... Can someone give me an explanation of how sliding windows are used for CNV analysis?  I.e., suppose I'm analyzing CNVs for chrI of s cerevisiae. I create a pileup, take the read depth at every base position, and then divide it by the average read depth. What would I do with a sliding window (e.g., ...
cnv sequencing written 5.5 years ago by anjali.gopal9150 • updated 5.5 years ago by Ying W4.0k
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Comment: C: No filtering occuring with GATK'S VariantFiltration Walker
... Yeah, this was the problem. I just figured it out too. Thanks! ...
written 5.6 years ago by anjali.gopal9150
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No filtering occuring with GATK'S VariantFiltration Walker
... (This has been x-posted to the GATK forum.) I have a file called rawSnps.vcf, which I've been trying to filter through the VariantFiltration Walker. The command I've been using is as follows: > /usr/java/latest/bin/java -Xmx2g -jar ~/bin/GenomeAnalysisTK-3.3-0/GenomeAnalysisTK.jar -T VariantFil ...
gatk written 5.6 years ago by anjali.gopal9150 • updated 5.6 years ago by Cherry50
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Extracting histogram data from CNVnator
... Hi, I just started using CNVnator to extract cnv information. I know that it allows us to visualize specific regions, but is there any way to extract information about the histograms as raw data? Has anyone tried this with root files? Any help would be much appreciated. Thanks!   ...
cnv written 5.7 years ago by anjali.gopal9150
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Comment: C: GATK vs more traditional SNP and alignment tools
... Thanks! I missed that GATK can't do general alignment. The remaining description helps a lot :) ...
written 5.9 years ago by anjali.gopal9150
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GATK vs more traditional SNP and alignment tools
... I've been asked to design an easy-to-use SNP caller at work (presumably for staff who don't know how to use a linux environment and would like the avoid the hassle of such). I've gone about doing this with some fairly traditional tools: bowtie2 for alignment, samtools and bcftools to modify sam file ...
alignment snp written 5.9 years ago by anjali.gopal9150 • updated 5.9 years ago by marina.v.yurieva520

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