User: KVC_bioinfo

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KVC_bioinfo350
Reputation:
350
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Location:
Boston
Last seen:
1 week, 4 days ago
Joined:
1 year, 1 month ago
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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 7 months ago by KVC_bioinfo350
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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 7 months ago by KVC_bioinfo350 • updated 7 months ago by Paolo220
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Comment: C: Error while using EdgeR
... I do not have NA. I used quantile normalization using Bioconductor. ...
written 7 months ago by KVC_bioinfo350
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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 7 months ago by KVC_bioinfo350
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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 7 months ago by KVC_bioinfo350
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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 7 months ago by KVC_bioinfo350 • updated 7 months ago by Pierre Lindenbaum113k
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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 7 months ago by KVC_bioinfo350 • updated 5 months ago by Kevin Blighe30k
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Comment: C: error using porechop on nanopore reads
... okay. thank you ill submit an issue there. ...
written 7 months ago by KVC_bioinfo350
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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 7 months ago by KVC_bioinfo350
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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 7 months ago by KVC_bioinfo350

Latest awards to KVC_bioinfo

Popular Question 10 weeks ago, created a question with more than 1,000 views. For Quartile Normalization in R : RNA-seq
Popular Question 10 weeks ago, created a question with more than 1,000 views. For Calculate length of sequences from fasta file
Popular Question 10 weeks ago, created a question with more than 1,000 views. For Human transcriptome download
Popular Question 10 weeks ago, created a question with more than 1,000 views. For Extracting randomly subset of fastq reads from a huge file
Popular Question 12 weeks ago, created a question with more than 1,000 views. For Post alignment QC of RNA-seq data
Popular Question 3 months ago, created a question with more than 1,000 views. For Post alignment QC of RNA-seq data
Popular Question 4 months ago, created a question with more than 1,000 views. For Quantile Normalization in R
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 5 months ago, created a question with more than 1,000 views. For Extracting randomly subset of fastq reads from a huge file
Popular Question 5 months ago, created a question with more than 1,000 views. For Extracting randomly subset of fastq reads from a huge file
Popular Question 5 months ago, created a question with more than 1,000 views. For Downloading gtf file for RefSeq
Voter 10 months ago, voted more than 100 times.
Scholar 11 months ago, created an answer that has been accepted. For A: Minimap2 warming message
Commentator 11 months ago, created a comment with at least 3 up-votes. For C: Selecting fastq sequences
Appreciated 11 months ago, created a post with more than 5 votes. For Tutorials for Library Normalization in DESeq2 and EdgeR
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