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Hello,
I am relatively new in variant calling using scRNA-Seq. I have 17 datasets from 17 patients. I want to call the variants for each patient. I only need the list of variants in each sample.
Can…
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We use merged platform because adding RNA-Seq data require that the same platform is used for all the samples. This is unnecessary because ultimately these platforms get replaced by a generic expressi…
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```
STAR --runThreadN 16 \
--genomeDir sheep/geneome/STAR/ \
--runDirPerm All_RWX \
--readFilesCommand zcat \
--outSAMtype None \
--soloType SmartSeq \
…
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Hi,
I have successfully used DISCOVER with data from whole-exome sequencing. I am wondering whether I can use it with data from targeted sequencing data generated by MSK IMPACT or DFCI OncoPanel. A…
jud-b updated
3 months ago
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conda is leveraged for installing (some) dependencies (at least, the recommended install method), but conda is not fully leveraged via a bioconda recipe for installing scNanoGPS.
Are there plans on…
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Hello everyone,I'm trying to conduct a mapping of my 10x scRNA-seq data with a customized reference genome using STARsolo.My analysis seemed to work properly ("finished successfully" message appeared)…
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Hi, thanks for developing such a useful tool!
Our lab is interested in applying the Optimized 10x method to AML scRNA-seq samples we already sequenced as part of a [recent publication](https://www.…
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Dear author,
Thanks for your excellent work. I have some VLP enrichment samples from the animal gut. When I use the tool, how to select the parameter "--enrichment_preset". The default is "human",…
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Hello,
Thanks for this package. I have a few quenstions about the data processing. For the droplet-based method, why we need to perform cellranger to obtain bam files and then use STARsolo? Can we…
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I ran a comparison in GENIE BPC NSCLC based on sequencing center: https://genie.cbioportal.org/comparison/alterations?comparisonId=640e86f371a4b769b9dda0c6
The top results on Genomic Alterations ar…