Tom Kelly
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Using Seurat to compare mutant vs.wt
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7 votes

Single-cell analysis to compare samples is a long a difficult process. There is very good documentation for 10x Genomics cellranger, the DropSeq Pipeline and the Seurat R package. These tools all have ...

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determining doublets in single-cell RNA-seq
4 votes

We cannot assume that doublets will produce more UMIs I would caution the assumption that all doublets will have twice the UMI levels of isolated single-cells. Many "doublets" could contain ...

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How to plot p-values in a circular barplot?
Accepted answer
3 votes

The adjustcolor function from grDevices can be used to generate colours with transparency. What you want is colours based on the pathway and transparency to form a colour gradient for the p-value. ...

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Volcano plot in R
3 votes

Without a minimal reproducible example (MWE), I can't reproduce the plot but I would suggest using existing volcanoplot functions such as the limma package on Bioconductor. Here is a typical workflow ...

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Script to allow gene set enrichment analysis of 10x genomics data in R
2 votes

There is no purpose-built R package to perform gene set enrichment analysis on single-cell data but there does not need to be. You should be able to tools developed for bulk-RNA-Seq or microarray data,...

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How to best detect the "peaks" in RNA-seq data that are not assigned to any gene?
2 votes

Many pipelines have been set up for this such as software developed for the FANTOM Project at RIKEN. The software for this is available from our website. These were set up for analysis of CAGE ...

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Separate boxplots for multiple violin plot
2 votes

The vioplot package comes built in with boxplots. You can download it from CRAN or there are more features (including formula input and separate colours) in the development version on GitHub: https://...

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What does an FDR value of 1 in RNA-seq mean?
2 votes

In practice, you can interpret it just like a p-value. An FDR value is a p-value adjusted for multiple tests (by the Benjamini-Hochberg procedure). It stands for the “false discovery rate” it ...

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How to create a .bed file from .fasta?
2 votes

Assuming that you have a reference genome sequence file (e.g., reference.fasta) available. Getting this kind of file is straightforward. 1) Index the reference genome and map your reads or FASTA ...

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plotting two heatmaps with the same order of genes
2 votes

You have 2 options provided that both datasets have the same genes (rows): Keep the original order of rows in the heatmap. If they’re in the same order in the dataset then they will be in the heatmap....

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Is it possible to merge scRNAseq data from experiments with different design?
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2 votes

It’s right there on the cellranger manual: #aggregate results of counts for separate samples cellranger aggr #analyse the combined results cellranger reanalyze Note: I’m not sure this applies to the ...

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How to identify gene expression signatures from gene expression data?
2 votes

Gene Signatures are sets of genes to report a consensus signal or function. They are not defined in a particular way but can be defined by any chosen group depending on the biological function that ...

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Percentage of each cluster in Seurat
1 votes

You can access these data from a Seurat object as columns of object@meta.data and tabulate them. There are functions such as “propellor” which will also implement this: https://github.com/Oshlack/...

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No counts for added gene in cellranger (scRNA-seq)
1 votes

The first column of your GTF must correspond exactly to the name of the sequence in your FASTA file. Typically this is the chromosome so a GTF line: chr1 hg38_knownCanonical exon 11106535 ...

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What kind of analysis can be done with differential expression of transcription factors?
1 votes

It sounds like you’ve already done differential expression analysis (with genes or transcripts) and a pathway enrichment analysis to find these. Differential expression of these functional groups is ...

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Normalizing microarray data for clustering heat map
1 votes

Negative values are to be expected as you have log-transformed the data. Any data value below 2 will have a negative log2. There is a difference between normalising for analysis and truncating for ...

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EMT/EMT-like processes in bioinformatics to study cancer progression
1 votes

The epithelial-mesenchymal is a process by which cells lose some of the structures specific to their cell type. This is normal during embryonic development or wound healing for the formation of new ...

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Files for paired end RNA sequencing
0 votes

Paired ends is a configuration in sequencing platforms. Illumina is the most popular at the moment and most single-cell sequencing is done using paired-end Illumina sequencing. It varies between ...

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How to run same command on multiple files?
0 votes

You can create a script to pass arguments to as follows: #! /bin/bash bwa mem -M -R "@RG\tID:${1}\tLB:${2}\tPL:ILLUMINA\tPM:HiSeq2000\tSM:${1}" ../ref/M._tuberculosis_H37Rv_2015-11-13.fasta ${1}_* &...

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Can I get the graph generated by cellranger
0 votes

Files in a cellranger run Cellranger removes the intermediary files after the clusters have been computed. This can be observed in the following path from the cellranger project directory. This ...

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Expression of a gene in different groups
0 votes

You can use the raw counts to normalise your data. It is import to do so before doing a differential expression analysis: otherwise you will detect more reads from samples with higher coverage and ...

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