It should be great if I have any assistance in my build up command using trinity package...

   I want reads in a specific short interval, but if I do that with samtools view I also get reads that are spliced over that interval.

   Hello, I would recommend following RSEM wiki for more information about the options, or even run RSEM directly, not with the script provided by Trinity.

   This seems like a model case for why we need better sustainable bioinformatics data and services. I don’t know the exact background behind this, but some things are obvious: The original author Horvath no longer works for the institution UCLA where the project was developed, He’s now...

   this is names.dmp: names.dmp and nodes.dmp nodes.dmp : media images cc a b b d c b : media images a c c b aa ed c

   Hi, I am studying gene expression studies with samples with trinity. I successfully completed abundance estimation using: samples file est method RSEM output dir in brief here . Then I got the following output folders with RSEM results Abl, Abl, Abl, Bn, Bn,...

   I am building the database of kraken . The previous add to library used my custom taxID and wrote names.dmp and nodes.dmp myself. When running kraken build build db ., the following prompt appears: Creating sequence ID to taxonomy ID map step ... Sequence ID to taxonomy ID...

   see also : https: www.biostars.org p ; https: www.biostars.org p ; https: www.biostars.org p

   what’s the gray section it’s the read you want do you only want the reads that end at the splice event single point location

   yes if there is more than one sample genotyped.

   Hi, I am looking at a rare splicing event, and would like to keep only reads in a specific interval that have an alignment at that location. With a simple samtools view alignment.cram chr : I also get all reads that are spliced across that interval screenshot below . How do I get...

   Hi, I am working with Xenium TMA data, and I want to subset each sample individually from the seurat object. The samples are from different organs, hence the subsetting. Please let me know if anyone knows how to subset. I can already do a fov zoom for each sample using x,y coordinates. Thanks...

   Is it typical to observe such a profile in the context of diploid organism

   I’d like to learn how to do a preservation analysis using WGCNA modules I’ve generated. However, the WGCNA tutorials and data seem to be offline. https: horvath.genetics.ucla.edu html CoexpressionNetwork ModulePreservation Tutorials Does anyone know where I can access the tutorial and the demo...

   Yes you can use ggplot to create your own plots from a table of results from a differential methylation analysis. You just need to adapt a general code for volcanoplots, heatmaps etc to your own data. There are also some good tutorials available on this forum that will help you to create such...

   This forum is not dedicated to this type of request, there are many online tutorials for creating heatmaps accessible with simple internet searches. If you have a more specific question related to the code you are using, then we will be able to help

   Hi Everyone, I have conducted DNA methylation analysis using the Limma and Minfi packages. However, I am struggling to generate plots for my methylation data. I am specifically interested in generating basic plots such as volcano plots, heatmaps, GO analysis plots, and bar plots. Should I consider...

   Download the CPC tool supported by python from here https: github.com gao lab CPC standalone releases tag v . . . Then follow the instructions: prequisits pip install biopython packages...

   I have an Illumina sequencing data . When I ran fastqc it did not show any column for kmer content. When i cleaned the data using bp as minimum length and q as the phred quality score , the fastqc report had an added column for failed kmer content . Why is it showing how to solve this.

   Hello everyone I have a list of pathways from GSEA analysis RNA Seq data and I want to plot a heatmap of genes associated with pathways, showing distinctly each pathway in the heatmap. Can somebody help me with this

   Hi the community I’ve recently written a toolkit which allows to annotate scRNA seq data directly from literature. It requires a raw adata file and a pdf file. Then It can automatically extract information from articles and do all downstream job like filter, preprocessing, clustering,...

   Hello. I want to merge Seurat objects and do batch correction. How can I do this I’m going to use the merge function to merge seurat objects. If there is another better way, please let me know.

   I don’t know enough about genomics files. I have a human tumor sample of bam, which used bwa and sambamba aglined and targged with duplicated reads. I used the below of commands converting the bam file to a wig file required by HMMcopy. path hmmcopy utils bin readCounter window ...

   let me know the scope and scale of the request e.g. I need to do this for every record in Pubmed and can help

   how is this query itself originating