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User: paulranum11

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paulranum11 • 70
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Posts by paulranum11

<prev • 38 results • page 1 of 4 • next >
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Comment: C: umi_tools count omitting majority of reads
... I confirmed that this was indeed what was happening. ...
written 7 months ago by paulranum11 • 70
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Comment: A: umi_tools count omitting majority of reads
... When I add the `--ignore-umi` option i get a similarly low number of reads (22,727). I will try to extract the number of counts and unique UMIs to confirm that this is not the issue. ...
written 7 months ago by paulranum11 • 70
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umi_tools count omitting majority of reads
... I am trying to use UMI tools to create a genes x counts matrix for a single-cell RNA-Seq dataset. This can be done using the `umi_tools count` command. Below are two (sam formatted) lines from my input file. Read assignment status is denoted using the XS flag and gene ID is denoted using the XT fl ...
rna-seq sequencing written 7 months ago by paulranum11 • 70
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Drug impact on gene expression database?
... Does anyone know of a database or bioinformatics resource of drug treated RNA-Seq datasets? I found remarkably few relevant resources google searching. [Galahad][1], the one resource I did find, appears to have their server down. I am interested in identifying drug candidates that upregulate th ...
rna-seq written 8 months ago by paulranum11 • 70 • updated 8 months ago by igor ♦ 11k
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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 10 months ago by paulranum11 • 70 • updated 10 months ago by Kevin Blighe ♦ 65k
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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 14 months ago by paulranum11 • 70
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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 14 months ago by paulranum11 • 70
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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 15 months ago by paulranum11 • 70 • updated 14 months ago by Artem Kiselev • 30
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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 15 months ago by paulranum11 • 70
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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 15 months ago by paulranum11 • 70

Latest awards to paulranum11

Popular Question 11 months ago, created a question with more than 1,000 views. For Seurat "Expression Level" units
Popular Question 18 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 3.7 years ago, created a question with more than 1,000 views. For cummeRbund Gene Sets
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