User: upendrakumar.devisetty

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Posts by upendrakumar.devisetty

<prev • 123 results • page 1 of 13 • next >
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Comment: C: Masurca assembly denovo
... Hi, I am getting the same error. Can you tell me how did you solved the issue? Thanks, Upendra ...
written 6 months ago by upendrakumar.devisetty350
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Comment: C: Extracting histogram data from CNVnator
... Have you found answer to this? I would like to know this well so that I can plot my histogram. Currently one cannot save the histograms in CNVnator. Thanks.. ...
written 20 months ago by upendrakumar.devisetty350
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Comment: C: Understanding VCF file for downstream analysis
... Ok. I will ask my collaborator. Thanks.. ...
written 2.1 years ago by upendrakumar.devisetty350
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Comment: C: Understanding VCF file for downstream analysis
... Is there a way to convert this to VCF file based on information in `INFO` column? ...
written 2.1 years ago by upendrakumar.devisetty350
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Understanding VCF file for downstream analysis
... I got this vcf file from my collaborator and I am so trying to understand this for the last few days but no avail. I needed to use this vcf for all downstream analysis such as Structure, PC, Linear Discriminant Analysis. I have worked with VCF files before but I never seen this kind before. #CH ...
vcf gatk snp written 2.1 years ago by upendrakumar.devisetty350
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difference between voom and calcNormFactor normalization methods for RNA-Seq analysis
... What exactly is the difference between between voom (limma) and calcNormFactor (edgeR) normalization methods? Though it is not very clear to me, i understand the "voom" normalization is better, but in some articles i see that people use both normalizations simultaneously. i.e calcNormFactor followed ...
voom limma rna-seq edger written 4.2 years ago by upendrakumar.devisetty350 • updated 3.0 years ago by Gordon Smyth780
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Comment: C: How to generate FPKM values for Velvet/Oases assembled transcripts
... Thanks for the modification. Appreciated ...
written 4.4 years ago by upendrakumar.devisetty350
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Comment: C: How to generate FPKM values for Velvet/Oases assembled transcripts
... Good point. I have the transcripts in bed format and probably can change them to gtf and use them but how about the bam file (accepted_hits.bam) file that is need as input with cufflinks ? Do you think i should map all the reads from which i generated transcripts from using TopHat and then run cuffl ...
written 4.4 years ago by upendrakumar.devisetty350
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Comment: C: How to generate FPKM values for Velvet/Oases assembled transcripts
... I have both reads and transcripts ...
written 4.4 years ago by upendrakumar.devisetty350
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How to generate FPKM values for Velvet/Oases assembled transcripts
... Hi, Can anyone point to me of how i can generate FPKM values for the Velvet/Oases assembled transcripts. I know TopHat/Cufflinks pipeline for generating FPKM values but in this case i already have Velvet/Oases assembled transcripts along with the reads. All i want to do is to see the expression lev ...
fpkm velvet/oases rna-seq written 4.4 years ago by upendrakumar.devisetty350 • updated 4.3 years ago by Biostar ♦♦ 20

Latest awards to upendrakumar.devisetty

Popular Question 19 months ago, created a question with more than 1,000 views. For difference between voom and calcNormFactor normalization methods for RNA-Seq analysis
Great Question 19 months ago, created a question with more than 5,000 views. For Trinity Transcriptome Assembly
Popular Question 19 months ago, created a question with more than 1,000 views. For How to generate FPKM values for Velvet/Oases assembled transcripts
Great Question 20 months ago, created a question with more than 5,000 views. For Trinity Transcriptome Assembly
Popular Question 22 months ago, created a question with more than 1,000 views. For difference between voom and calcNormFactor normalization methods for RNA-Seq analysis
Student 23 months ago, asked a question with at least 3 up-votes. For difference between voom and calcNormFactor normalization methods for RNA-Seq analysis
Popular Question 23 months ago, created a question with more than 1,000 views. For difference between voom and calcNormFactor normalization methods for RNA-Seq analysis
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