Sierra

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Changes in gene 3'UTR length

1

Hello, how to evaluate changes in gene 3'UTR length?

TianYu-828

Interpretation of log2 fold changes in the result

1

Hi, thank you for providing such a great tools. I am currently analzying UTR length shift using the function "DetectUTRLengthShift". Among the parameters of DetectUTRLengthShift function, you can specify population.1...

Kyung-TaeLee

Hi, I'm trying to plot the identified peaks back to my Seurat UMAP using PlotRelativeExpressionUMAP function, but many cells are buried in the UMAP plot. Seurat's FeaturePlot function has an...

ckong18

Error in PlotRelativeExpression functions

1

Hello everyone, I am using Sierra and I keep getting this error for all PlotRelativeExpression functions (TSNE, UMAP, Box). `error in apply(expression.set, 1, function(x) { : dim(x) must have a...

hkarakurt8742

Error when running CountPeaks

8

I get an error when using the CountPeaks function for one of my samples: ``` There are 14963 whitelist barcodes. Import genomic features from the file as a GRanges object...

idupanloup

Getting "Error in (function (x) : attempt to apply non-function"

3

Hi @rj-patrick. I came across the message, "Error in (function (x) : attempt to apply non-function", when running count peaks as shown below. CountPeaks(peak.sites.file="merged_peaks.txt", gtf.file="", bamfile="", whitelist.file="", output.dir="out_dir", countUMI=TRUE, ncores=10)`...

alanlamsiu

issues with generating splice junction file

7

I have 3' scRNAseq data from 10X genomics. I ran the data through cellranger so, I have the possorted bam ouput file. I tried to run regtools on the bam...

ckong1806

I would like to plot a umap where cells show their 3'UTR usage of all genes in a color-coded manner. Is it possible to create this plot from the analysis...

ntsopoul

Sierra dataframe has 0 length

1

Hi everyone: I met a problem when I run the DUTest as below, so I find my peaks.seurat@tools$Sierra doesn't have any thing except the rownames. > res.table = DUTest(peaks.seurat, +...

top334

DUTest function Error

1

Hello, I am using Sierra and I replicated all results from vignette. I tried to use with my own data with same steps but in DUTest step I have an...

hkarakurt8742