Kohl Kinning
  • Member for 4 years, 8 months
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Hosting IGV web on a server
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5 votes

You can use X11 forwarding to run IGV on the headless server where the data is located and simply forward the GUI to your client machine using the X11 protocol. This is a solution I use consistently ...

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Output of Seurat FindAllMarkers parameters
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3 votes

pct.1– The percentage of cells where the gene is detected in the first group p_val_adj– Adjusted p-value, based on bonferroni correction using all genes in the dataset. This is not also known as a ...

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Seurat FindMarkers() output, percentage
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3 votes

Your interpretation of pct.1 and pct.2 is misguided. If pct.1 == 1, the given gene was detected in all of the cells. This carries no information about high expression or low expression in the cell, ...

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How can I not show insertions in the Integrative Genome Viewer (IGV)?
3 votes

Preferences -> Alignments -> Hide indels < 'x' bases. Credit to Pierre Lindenbaum

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Changing the name of elements in a column
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3 votes

If your data is in a dataframe you can make use of plyr. Using mapvalues() from this library, you can rename provide a list of keys and a list of values. Instead of explicitly listing the keys, we can ...

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Protein SCA and DCA
3 votes

While my suggestion doesn't technically fit your qualifications, I do think it may be useful. I bring this up because you mention you want to continue with your R workflow. I am assuming you don't ...

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Issue with visualising cladogram/phylogenetic tree with multiple sequence alignment data in R?
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3 votes

You were very close, you just need to supply the offset argument to msaplot(). So using your code block above with one extra argument in msaplot() library(tidyverse) library(ggtree) library(seqinr) ...

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Build a Pubmed query given long gene list
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3 votes

After getting it out on paper (so to speak) I was able to accomplish what I wished with bash: #!/bin/bash gene_list=($(cat ./markers_clean.txt)) query=${gene_list[@]:0:1} parens="(" for gene in ${...

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Changing a wide range of colours to a limited gradient
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3 votes

If you would like to color discrete intervals on a gradient as opposed to having a continuous gradient (like your second plot), use this approach. It is similar to the approach in the answer I ...

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Changing a wide range of colours to a limited gradient
3 votes

TSNEPlot() TSNEPlot() will always treat your variables as discrete. My approach is to manually generate a gradient with unique colors for each factor level and pass it to the cols.use argument in ...

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Using external list of PCs for clustering
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3 votes

There is a way to do this, and even better--there is documentation for how to do it! No surprise coming from the Satija Lab. In the vignette they perform multidimensional scaling, but the idea is the ...

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Difference between samtools mark duplicates and samtools remove duplicates?
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3 votes

samtools rmdup and samtools markdup -r do the same thing. Without the -r flag samtools markdup only flags the duplicates. You'll have to run samtools fixmate -m and sort the output to add ms and MC ...

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Increase number of threads for GATK 4.0 HaplotypeCaller
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3 votes

I am assuming you are using the non-SPARK version of the method. To specify the number of threads you wish to use with HaplotypeCaller, include --native-pair-hmm-threads (documentation). This will ...

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How to compare transcriptomic profiles of two cell types (single cell RNA-seq)?
3 votes

You are looking for a way to compare expression profiles between cell types, and your data is counts of genes expressed per cell. Your issue is that the data is highly dimensional. It has as many ...

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Subsetting of object existing of two samples
2 votes

I think your issue is simply not assigning the newly-subset object in to a new object. Assuming rownames(subset_DR1) is indeed a list of cell names seuratObj_subset_dr1 <- SubsetData(seuratObj, ...

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Can I get the graph generated by cellranger
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2 votes

Cell Ranger You can't download the tSNE coordinates for cells directly from the Analysis tab of the fancy, polished .html document that Cell Ranger produces. If you have access to the machine on ...

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ScaleData() from Seurat causes crash on RStudio Cloud
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2 votes

It seems RStudio server doesn't know it's limitations. Currently, Projects are limited to 1GB of RAM. Using the R package ulimit which mirrors the function of ulimit and allows implementation of ...

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How to run MaxQuant in command line mode?
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2 votes

Give mono MaxQuantCmd.exe [OPTIONS] a try. University of Oslo description of how to use the tool in their infrastructure.

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High Phred Quality score VCF file
2 votes

See this post on the GATK forums. It is normal to see values above 255. The QUAL score is the posterior probability that all samples in your callset are homozygous reference. I quote Sheila's ...

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Genotyping with Illumina HumanOmni1-Quad before whole genome sequencing
2 votes

The Illumina HumanOmni1-Quad beadchip is a microarray device consisting of 1,140,419 markers which have derived from the 1,000 genomes project. The markers chosen are is high-value regions of the ...

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Is there a way to tell which chromosome a gene is on, by looking at the "Chromosome/scaffold name"
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2 votes

What you are looking at is a patch, not an actual chromosome location. HG-2128 is an issue ID, something that the Genome Reference Consortium uses to track issue with references. Information regarding ...

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Can we describe synthetic biological sequence data as belonging to a "species" or "taxon"?
2 votes

When looking at genomic data for bacteria, taxa above the species level are operational taxonomic units (OTUs). OTUs are designated based on percent identity of the sequence (specifically the 16S rRNA ...

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how to change the PC use in the dimplot and feature plot
1 votes

You can choose which PC dims to plot by specifying the dims argument within the functions. To use PC-4 and PC-5, DimPlot(object = pbmc_small, dims = c(4, 5), reduction = "pca") and FeaturePlot(...

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AutoDock 4 -soft docking
1 votes

The smooth parameter is an optional keyword and command that changes the smoothing potential. If not provided, the default is 0.5 angstroms by default. Try passing 0 with this keyword in the AutoGrid ...

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In calculating the retention index, why do we use the character state with the lowest frequency?
1 votes

The maximum number of steps (or changes) is the number of taxa with state 1 or 0, whichever is smaller. Conceptually, this is the number of character changes if each taxon evolved its state ...

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Source for whole genome comparisons at NCBI Genomes
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1 votes

I inquired into the details of the dendrograms after becoming frustrated with the lack of information. As with Ensembl, I'm sure that the folks at NCBI have a standardized pipeline that they run the ...

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chromPlot R package: remove scales
1 votes

Setting the legChrom argument to NA will omit plotting a legend. Found in the manual for chromPlot on Bioconductor for release 3.7.

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Compare clusters from different datasets
1 votes

I've been working with the multi-CCA alignment workflow in the Seurat package and am very impressed with functionality. As usual, the CCA tutorial is excellent for an alignment workflow and will get ...

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Convert Cotton Probe ID to Gene Symbol
1 votes

Your dataset was produced on a microarray. The probe IDs in the FASTA file are similar to read IDs produced from other NGS experiments like RNA-Seq. According to the workflow provided by Ensembl the ...

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Batch detection of CRISP proteins in fasta file
1 votes

Is your goal to detect the actual proteins from the sequences? If you'll settle for detection of transcripts from the genes encoding these proteins as opposed to detection of the proteins themselves, ...

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