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User: paulranum11

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paulranum11 • 40
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40
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3 days, 4 hours ago
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2 years, 11 months ago
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Posts by paulranum11

<prev • 34 results • page 1 of 4 • next >
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DEseq2 Shade PCA plot by gene counts
... Hi All, I am working with DEseq2 to do some RNA-Seq analysis and would like to find a solution for displaying the expression level of individual genes on the PCA plot. This functionality exists built into other packages like Seurat (using "FeaturePlot"). Does anyone know of a way to implement t ...
ggplot2 pca deseq2 heatmap written 3 days ago by paulranum11 • 40 • updated 2 days ago by Kevin Blighe ♦ 51k
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Comment: C: FeatureCounts count reads per gene (Including Introns)
... This is what i ended up doing. It was easy to make this SAF format file using biomart from ensembl.org. For future readers the columns to include for this format are: GeneName, Chromosome, GeneStart, GeneEnd, Strand Note that the column names header needs to be removed before the SAF file is used ...
written 4 months ago by paulranum11 • 40
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FeatureCounts count reads per gene (Including Introns)
... Hi Everyone, I am using `featureCounts` to count the number of reads mapping to genes. featureCounts -a $myGTF \ -o counted_output \ -R BAM Aligned.sortedByCoord.out.bam \ -T $NUMCORES \ -M The a ...
featurecounts rna-seq written 4 months ago by paulranum11 • 40
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How to access STAR index loaded into shared memory
... I am trying to run STAR in a shared memory environment. I want to load a single copy of the genome index and then run star multiple times using that pre-loaded index. However I don't seem to be passing the pre-loaded index to STAR correctly. When I run the following, one index is loaded for each ...
alignment star rna-seq written 4 months ago by paulranum11 • 40 • updated 3 months ago by Artem Kiselev • 20
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Comment: C: STAR genomeLoad issue
... I think that i am not properly telling STAR to use the loaded index because when run it as shown (with --genomeDir $STARINDEX) a index file is loaded for every input.fastq in the loop and the system runs out of memory. However when i omit the (--genomeDir $STARINDEX) i get an error saying that the ...
written 4 months ago by paulranum11 • 40
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Comment: C: STAR genomeLoad issue
... How do you access the loaded index in the looped call to the star aligner? It seems that STAR is not using my loaded genome correctly. I have tried several configurations of the following with and without the --genomeDir flag. STAR --genomeLoad LoadAndExit --genomeDir $STARINDEX for file ...
written 4 months ago by paulranum11 • 40
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Comment: C: Kallisto "pseudo" output to counts/expression matrix
... tximport does not support this kallisto "pseudo" format output. ...
written 8 months ago by paulranum11 • 40
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Comment: C: Kallisto "pseudo" output to counts/expression matrix
... The output of kallisto "pseudo" is formatted differently than the output of other kallisto runs i have performed in the past (kallisto "quant" etc). The output appears to be associative arrays (matrix.tsv, matrix.ec, and matrix.cells). Here are some examples: `matrix.tsv` 12531 0 1 18862 ...
written 8 months ago by paulranum11 • 40
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Kallisto "pseudo" output to counts/expression matrix
... Is there a tool available that will convert the output of kallisto "pseudo" (matrix.tsv, matrix.ec, and matrix.cells) into a standard genes by cells counts matrix? ...
alignment rna-seq written 8 months ago by paulranum11 • 40 • updated 8 months ago by h.mon ♦ 28k
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Seurat "Expression Level" units
... I am trying to understand what the correct units are for the violin plots output by Seurat. The Y axis is labeled "Expression Level" by default on their violin plots. If I input a matrix of counts values will my units then be log counts? likewise, if i input a matrix of TPM values will the units b ...
rna-seq written 8 months ago by paulranum11 • 40 • updated 8 months ago by Friederike ♦ 5.2k

Latest awards to paulranum11

Popular Question 20 days ago, created a question with more than 1,000 views. For Seurat "Expression Level" units
Popular Question 7 months ago, created a question with more than 1,000 views. For SPLiT-Seq Demultiplexing a bash tool for extraction of barcoded single cells
Popular Question 2.8 years ago, created a question with more than 1,000 views. For cummeRbund Gene Sets
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