User: Palgrave

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Palgrave20
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Posts by Palgrave

<prev • 26 results • page 1 of 3 • next >
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DimPlot: labels clusters with sample name
... I am plotting a Seurat object and wonder how to label the samples in the output plot. I have a total of 5 samples across 1000 cells, and want to show which sample the different clusters belong. For instance if one clusters is mainly from one samples DimPlot(pbmc, reduction = "umap") ...
R rna-seq seurat sequencing written 1 day ago by Palgrave20 • updated 1 day ago by _r_am31k
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Differentially expression from a TPM-normalized single-cell data frame
... I have downloaded an expression matrix from a single-cell experiment that is already TPM normalized. What is the correct way yo preceded to detect differentially expressed genes based on this matrix? Does it have to be normalized further or can I use it directly as input in for instance Limma? ...
R forum next-gen rna-seq sequencing written 15 days ago by Palgrave20 • updated 15 days ago by ATpoint42k
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(Closed) low overlap using hugene10stprobeset
... I am trying to map my affy data IDs using the package **hugene10stprobeset.db**, but I only get an overlap for about 200 gene names. Am I using the wrong probeset? mydata: > mRNA.affy[,1:5][1:5,] ID_REF GSM409113 GSM409114 GSM409115 GSM409116 1 7892501 2.868901 8.338831 7.382 ...
R microarray affymetrix written 3 months ago by Palgrave20 • updated 3 months ago by GenoMax92k
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Convert ID for Human Gene 1.0 ST Array
... Hi, I am looking for a R package to convert IDs for the 1.0 ST array from affymetrix. The IDs have the format below: 7892501 7892501 ... ...
R microarray affymetrix written 3 months ago by Palgrave20 • updated 3 months ago by GenoMax92k
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Comment: C: Get splice-read counts from STAR-output
... But how do I identify only the reads overlapping a splice junction from the sam file? ...
written 9 months ago by Palgrave20
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Comment: C: Get splice-read counts from STAR-output
... Which bam file should I use? I get to mapping files: *Aligned.out.sam and *Chimeric.out.sam ...
written 9 months ago by Palgrave20
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Get read counts for reads overlapping exon-intron junction from STAR-output
... Hi, I am looking for a method to get counts per gene for the spliced read output from the *.tab files from STAR. Is there a way to do this directly in STAR? ...
star rna-seq written 9 months ago by Palgrave20
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Comment: C: Align two fasta files against each other
... I have two large files containing about 10000 fasta sequences. I would like to output one alignment for each sequence in File1. I guess command line blast is better? What parameters should I use? ...
written 15 months ago by Palgrave20
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Comment: A: Find 3'UTRs for species
... Are you sure? Ensembl Genes Genomic Sequence Sequence Retrieval Region Options: Promoter/Upstream by bases 5' UTR Exons CDS Exons 3' UTR Exons Introns Downstream by bases One FASTA record per gene. One FASTA record per region (exon, intron, etc.) wi ...
written 15 months ago by Palgrave20
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Align two fasta files against each other
... I have two files File1.fa and File2.fa that I would like to align against each other. I would like to print only the alignment result for File1 and leave a gap (-) where File1 does not align to File2. Which tools and parameters would you choose? ...
alignment written 15 months ago by Palgrave20

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Popular Question 4.8 years ago, created a question with more than 1,000 views. For miRNA isomiR analysis using Biostrings
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