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Hi guys,
I was looking pipelines to detect variant with cancer RNA-seq data (STAR-2pass bam files). After giving a look to opossum-platypus, gatk and DeepVariant pipelines I found Octopus.
Is i…
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Andrew, is it still an issue for cufflinks to deal with duplicate reads?
Tom and Bob noticed some jobs may be stalling and found this patch:
https://groups.google.com/forum/#!topic/tuxedo-tools-user…
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Hi Im running braker on the cluster using both protein data and RNA-seq data.
For the RNA-seq data we have around 300 different individuals, so I am randomly selecting only 50 individuals to run bra…
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Hello!
When I was using scTE, I encountered some problems and I wonder if I can get some advice.
### Question 1: Preprocessing BAM Files with Filtered Barcodes from CellRanger Output
I'm ex…
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I am running the latest version (v2.2) of ScanNeo and VEP (v106.1), and successfully complete the first step. However, I got some error messages by running the second step of the workflow below:
Than…
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Hi, as discussed in our recent meeting, we can work with custom dataloaders within scvi-tools. It requires being a torch DataModule that loads dictionaries of keyword arguments for each mini batch. We…
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More and more RNAseq is being used to call CNVs particularly from single-cell data (e.g. inferCNV). However, expression compensation, noising expression, and fine differences in gene expression confou…
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## Is your feature request related to a problem? Please describe
I think it would be good to have [SoupX](https://github.com/constantAmateur/SoupX) or a similar tool as part of the pipeline.
…
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Thanks for your useful tools for scRNA analysis!
I just want to know for sure about input of run_de function when using a Seurat object:
Is input raw counts or "RNA" assay when de_family = "single…