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Hello,
I have a question about measuring the concordance between bulk and sc DE tables. In your script, you used 6 different methods to generate DE tables when the input is bulk RNA-seq data. Whic…
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Hi Phil,
I was wondering if you could add Rail-RNA to MultiQC. Below is the requested info:
* **Name of tool:**
* Rail-RNA
* **Tool description:**
* Rail-RNA is a spliced alignment pr…
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Hi there!
I am performing an analysis with rMATS on our RNA-seq samples. I was wondering if the algorithm takes into account also the junction fragments (mates of the same fragment that maps in two…
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Hello,
I have some clusters with differentially expresses genes generated using Seurat. I also have a highly curated gene list and I wish to perform enrichment analysis using these on each cluster …
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I think it would be great if the samplesheet could handle additional columns (which would be ignored by the RNA-seq pipeline, but would be used by some downstream analysis). Keeping these in a separat…
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Project Title: Single-cell RNA-seq analysis of human pancreas from healthy individuals and type 2 diabetes patientsProject Short Name: Healthy and type 2 diabetes pancreasProject UUID: ae71be1d-ddd8-4…
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Hi Kipp,
I have met another issue when I analyzed my data (stranded total RNA-Seq) from FASTQ files. Only 9 circRNAs were detected but previously using BAMs as the starting point I found more than …
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https://doi.org/10.1101/262501
> Recent advances have enabled gene expression profiling of single cells at lower cost. As more data is produced there is an increasing need to integrate diverse data…
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**tl;dr**: 3-tag sequencing methods for bulk RNA samples contain known sample indices and UMIs and thus resembles sc-RNA-seq read formats. Do you have a recommendation on how to use Salmon and / or Al…