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User: KVC_bioinfo

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KVC_bioinfo • 350
Reputation:
350
Status:
Trusted
Location:
Boston
Last seen:
2 months, 1 week ago
Joined:
1 year, 3 months ago
Email:
k**************@gmail.com

Posts by KVC_bioinfo

<prev • 272 results • page 1 of 28 • next >
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Comment: C: Bioconductor: quantile normalization
... Thanks! I have looked them. However, I could not find how it works with low expressed genes. ...
written 9 months ago by KVC_bioinfo • 350
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Bioconductor: quantile normalization
... Hello All, I have used Bioconductor ‘preprocessCore’ fro quantile normalization. I am trying t understand how does it work with low expressed or zero count genes. Is someone aware of that? TIA ...
normalization biocinductor written 9 months ago by KVC_bioinfo • 350 • updated 9 months ago by Paolo • 220
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Comment: C: Error while using EdgeR
... I do not have NA. I used quantile normalization using Bioconductor. ...
written 9 months ago by KVC_bioinfo • 350
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Comment: C: Error while using EdgeR
... edgeR.DGElist <- DGEList(counts = raw.data.m , group = sample_info.edger ) causes error. raw.data.m was a typo sorry about that ...
written 9 months ago by KVC_bioinfo • 350
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Error while using EdgeR
... Hello All, I am trying to do differential expression using voom package. I constantly get the following error: > Error in .isAllZero(counts) : count matrix must be integer or > double-precision Below is the code I am trying: library(limma) library(preprocessCore) li ...
edger written 9 months ago by KVC_bioinfo • 350
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Extracting longest read from fastq file
... Hello All, I want to extract the longest read from a fastq file. I am not aware of any way to do it. Could someone help me here? TIA ...
fastq written 9 months ago by KVC_bioinfo • 350 • updated 9 months ago by Pierre Lindenbaum ♦ 115k
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Changing the legend names: R
... Hello all, ggplot(dataset, aes( x = Norm, fill = Condition, y=log2(measure))) + geom_boxplot() + scale_fill_manual(values=c("brown1","darkolivegreen4","burlywood3")) + theme_classic() + labs(title="Comparison",x="Norm", y = "counts") + scale_fill_continuous(labels ...
R ggplot2 written 9 months ago by KVC_bioinfo • 350 • updated 7 months ago by Kevin Blighe ♦ 33k
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Comment: C: error using porechop on nanopore reads
... okay. thank you ill submit an issue there. ...
written 9 months ago by KVC_bioinfo • 350
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error using porechop on nanopore reads
... Hello all, I am trying to use porechop for adaptor trimming on nanopore reads. I constantly get the following error: Error: input_reads.fastq could not be parsed - is it formatted correctly? I double checked the file. It is fine. I am using the following command: porechop -i input_reads. ...
porechop nanopore written 9 months ago by KVC_bioinfo • 350
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aligner for 1D^2 oxford nanopore data
... hello, I am wondering if anyone has tried aligning 1d^2 RNA-seq data. I am trying that on minimap2. It is giving me very low ~50% of mapped reads. it gives ~95% mapped reads for 1D. I am using the following command for 1d and 1d^2: minimap2 -ax splice -uf -k14 ref.fa direct-rna.fq > aln.sa ...
minimap2 1d^2 nanopore written 9 months ago by KVC_bioinfo • 350

Latest awards to KVC_bioinfo

Popular Question 4 months ago, created a question with more than 1,000 views. For Quartile Normalization in R : RNA-seq
Popular Question 4 months ago, created a question with more than 1,000 views. For Calculate length of sequences from fasta file
Popular Question 4 months ago, created a question with more than 1,000 views. For Human transcriptome download
Popular Question 4 months ago, created a question with more than 1,000 views. For Extracting randomly subset of fastq reads from a huge file
Popular Question 4 months ago, created a question with more than 1,000 views. For Post alignment QC of RNA-seq data
Popular Question 5 months ago, created a question with more than 1,000 views. For Post alignment QC of RNA-seq data
Popular Question 6 months ago, created a question with more than 1,000 views. For Quantile Normalization in R
Popular Question 6 months ago, created a question with more than 1,000 views. For Extracting randomly subset of fastq reads from a huge file
Popular Question 7 months ago, created a question with more than 1,000 views. For Extracting randomly subset of fastq reads from a huge file
Popular Question 7 months ago, created a question with more than 1,000 views. For Extracting randomly subset of fastq reads from a huge file
Popular Question 7 months ago, created a question with more than 1,000 views. For Downloading gtf file for RefSeq
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Scholar 13 months ago, created an answer that has been accepted. For A: Minimap2 warming message
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