User: venkateshr89

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venkateshr89710
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Posts by venkateshr89

<prev • 58 results • page 1 of 6 • next >
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Comment: C: Bed file with the snoRNA coordinates
... hi wwarner1 did you get to find the source for getting the SNORNAs bed?? I am trying to find the same since I wanted to remove exclude these regions from my BAM. ...
written 22 months ago by venkateshr89710
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Answer: A: what is the biological replications
... Biological replicates are parallel measurements of biologically distinct samples that capture random biological variation, which may itself be a subject of study or a noise source. Technical replicates are repeated measurements of the same sample that represent independent measures of the random noi ...
written 3.0 years ago by venkateshr89710
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Answer: A: split large vcf into user defined regions
... You can use vcftools. http://vcftools.sourceforge.net/man_latest.html The command should look like this `path-to-vcftools/ --vcf yourfile.vcf --bed filewith300regions.txt --recode --out outputfile.vcf` ...
written 3.2 years ago by venkateshr89710
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Comment: C: For RNAseq, is it mandatory to have approximately the same number of reads betwe
... You can use fastqc and also IGV browser to check the coverage. You can further use HTseq counts and dexseq_counts.py scripts to get the exon counts. I don't know your hypothesis so I am afraid if I can answer your question. Thanks ...
written 3.2 years ago by venkateshr89710
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Answer: A: For RNAseq, is it mandatory to have approximately the same number of reads betwe
... It is not mandatory to have same number of reads between any two comparison sets. As long as you have a decent coverage you are good to start with the analysis. With regards to RNAseq experiments replicates are much more important than the depth. Please refer to this paper http://www.nature.com/ ...
written 3.2 years ago by venkateshr89710
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Answer: A: Find Genotype concordance
... I found an answer. Thought this might help someone! You can use snpsift tools to do this > java -jar SnpSift.jar concordance -v file1.vcf file2.vcf > concordance.txt will do the job for you. This gives the concordance and discordance counts per SNP and also per sample. You can find the ...
written 3.2 years ago by venkateshr89710
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Answer: A: Trouble after imputation with minimac
... I's and D's just tells you that the data is imputed and on that particular locus it is an Insertion/Deletion. If you don't want this you can remove indels using [vcftools][1] --remove-indels. This will get rid of all the multiallelic sites. You then will be able to convert them to plink PED/MAP. Go ...
written 3.3 years ago by venkateshr89710
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Comment: C: Find Genotype concordance
... Dr. Lindenbaum, I tried using GATK Genotype Concordance which summarizes. This gives summary stats for concordance rate across Samples. But I am looking for summary of concordance rate across SNPs. Is there an alternate way to do this? Thank You and your help is much appreciated ...
written 3.3 years ago by venkateshr89710
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Find Genotype concordance
... Hi, I had to compare variant calls from two different arrays. Exome sequence and OMNI chip. I found genoytpe concordance per sample (sample based Genotype concordance) using "GATK Genotype concordance". The output is shown below which gives overall genotype concordance per sample. Sample ...
genome gatk next-gen snp sequencing written 3.3 years ago by venkateshr89710
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Comment: C: Phred 33 and phred 64 scores mixed in .bam file
... Ryan, Thanks for the reply. The data is pretty old. It came from SOLID sequencing. It was later aligned using Novoalign. ...
written 5.3 years ago by venkateshr89710

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Popular Question 19 months ago, created a question with more than 1,000 views. For Estimatelog2Foldchange In Dexseq
Great Question 3.0 years ago, created a question with more than 5,000 views. For Remove Duplicate Individuals From Plink Ped File Using Plink
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Teacher 5.9 years ago, created an answer with at least 3 up-votes. For A: What Do You Waste Your Time On
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