User: komal.rathi
komal.rathi • 3.7k
- Reputation:
- 3,700
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- Location:
- Children's Hospital of Philadelphia, Philadelphia, PA
- Website:
- https://github.com/kom...
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- komalsrathi
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- Last seen:
- 1 month, 2 weeks ago
- Joined:
- 7 years, 9 months ago
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- k**********@gmail.com
Posts by komal.rathi
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2
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353
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2
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... Someone posted an answer to this on stackoverflow which I am sharing here:
https://stackoverflow.com/a/63017471/1844024
To get the correct dendrogram, you need first to reorder the columns of tmp according to the information given in `pcahcpc.tree$labels`.
idx <- as.numeric(gsub("col_","", ...
written 6 months ago by
komal.rathi • 3.7k
0
votes
2
answers
353
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2
answers
... The pcahcpc.tree seems to be a valid hclust object:
> class(pcahcpc.tree)
[1] "hclust" ...
written 6 months ago by
komal.rathi • 3.7k
2
votes
2
answers
353
views
2
answers
... Cross posted: https://stackoverflow.com/questions/62972420/hclust-object-from-factorminer-does-not-cluster-dendrogram-in-pheatmap
I am trying to create a heatmap of a matrix with 20 rows and 10 columns using `pheatmap::pheatmap`. To cluster the columns, I am using an `hclust` object obtained after ...
written 6 months ago by
komal.rathi • 3.7k
0
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2
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1.9k
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2
answers
... What versions of STAR/RSEM are you using?
Also, can you do a `tree` (or show the directory structure) on your working directory? I see you have hardcoded the paths of `bam/, fastq/ and quant/`. Just want to make sure these directories exist. ...
written 14 months ago by
komal.rathi • 3.7k
0
votes
4
answers
6.7k
views
4
answers
... Can you move this to an answer so I can accept it? Thanks! ...
written 15 months ago by
komal.rathi • 3.7k
4
votes
1
answer
1.7k
views
1
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... I got a response from the UCSC Genome Browser help desk which resolved my question:
> The knownCanonical gene set is created from the longest transcript of
> the basic Gencode gene set. This convention was not around for the V23
> gene set, so that file does not exist. If you would like to ...
written 20 months ago by
komal.rathi • 3.7k
1
vote
1
answer
1.7k
views
1
answers
... Thanks, I will do that. I will keep this open and post any responses I get from the help desk. ...
written 20 months ago by
komal.rathi • 3.7k
5
votes
1
answer
1.7k
views
1
answer
... Hi,
I am using UCSC genome browser to get known canonical transcripts using this [link][1]. This is the default Gencode version V29 and I am able to set the `table` to `knownCanonical`. However, when I change the gencode version to `ALL Gencode V23` under `track`, the table options change and I can ...
written 20 months ago by
komal.rathi • 3.7k
0
votes
2
answers
3.1k
views
2
answers
... I ended up doing a chisq test using the output of ASEReadCounter. ...
written 2.0 years ago by
komal.rathi • 3.7k
0
votes
0
answers
2.4k
views
0
answers
Comment:
C: RSEM output interpretation
... I am using the following parameters:
rsem-calculate-expression \
--paired-end \
--no-bam-output \
--quiet \
--no-qualities \
-p {threads} \
--forward-prob 0.5 \
--seed-length 25 \
--fragment-length-mean -1.0 \
--bam {bam} {genomedir} {prefix} ...
written 2.2 years ago by
komal.rathi • 3.7k
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For TCGA: What are mRNA expression z-scores? Does TCGA have mRNA expression from controls?
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For C: DEXSeq with cufflinks gtf file
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For Calculate The Frequency Of Nucleotides At Each Position In An Mpileup File
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For C: DEXSeq with cufflinks gtf file
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For DESeq and Limma+Voom Normalization for Rna-Seq Data Using Ercc Spike-In
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For How to remove reads with hard/soft clipping along with its mate?
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For How to sort fastq.gz files efficiently
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For How to sort fastq.gz files efficiently
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For C: have difficults using htseq count
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For A: How the best way to verify the up and down regulated genes in a list of DE genes
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For C: have difficults using htseq count
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For How to sort fastq.gz files efficiently
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For C: DEXSeq with cufflinks gtf file
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For How To Get Mapping Statistics On Bam File
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For A: Error in htseq-count: "Malformed SAM line: MRNM == '*' although flag bit &0x0008
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For A: cufflink and cuffmerge error
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For DESeq and Limma+Voom Normalization for Rna-Seq Data Using Ercc Spike-In
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17 months ago,
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For How to sort fastq.gz files efficiently
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17 months ago,
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For How to sort fastq.gz files efficiently
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19 months ago,
created an answer with at least 3 up-votes.
For C: have difficults using htseq count
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19 months ago,
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For A: cufflink and cuffmerge error
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