User: KVC_bioinfo
KVC_bioinfo • 320
- Reputation:
- 320
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- 11 months, 4 weeks ago
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Posts by KVC_bioinfo
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... Thanks! I have looked them. However, I could not find how it works with low expressed genes. ...
written 5 months ago by
KVC_bioinfo • 320
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... 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 ...
written 5 months ago by
KVC_bioinfo • 320
• updated
5 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 5 months ago by
KVC_bioinfo • 320
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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 5 months ago by
KVC_bioinfo • 320
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... 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 ...
written 5 months ago by
KVC_bioinfo • 320
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... 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 ...
written 5 months ago by
KVC_bioinfo • 320
• updated
5 months ago by
Pierre Lindenbaum ♦ 111k
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5 follow
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... 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 ...
written 5 months ago by
KVC_bioinfo • 320
• updated
4 months ago by
Kevin Blighe ♦ 26k
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... okay. thank you ill submit an issue there. ...
written 5 months ago by
KVC_bioinfo • 320
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... 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. ...
written 5 months ago by
KVC_bioinfo • 320
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... 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 ...
written 5 months ago by
KVC_bioinfo • 320
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