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### Project short name:
BenchmarkingSingleCellProtocols
### Primary Wrangler:
Ami
### Secondary Wrangler:
Ida
### Associated files
* Google Drive:
https://drive.google.com/drive/folders/10XD1BCC9…
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SmartSeq2 data should appear at the plate level in a given row of the browser, rather than at the single cell level.
Plate information is available in the metadata.
This better corresponds to 10X row…
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Hi!
I was wondering if you could please advise on how to rectify the error below? Many thanks!
library(Seurat)
library(SeuratData)
InstallData("panc8")
data("panc8")
…
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I am finding an error when I am trying to run the kb count command with the -tcc option to count isoform expression from SMARTSEQ2 data. I am running the command with data from 15 samples in the batch…
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Dear @andreariba,
I find this concept very appealing, and I am currently trying to implement it for my SmartSeq2 data. I am an R person, and very unused to python, so my issues are probably easy to …
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https://mp.weixin.qq.com/s/mQCAEHyq4R46KFKtn6SPDA
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Hello,
Great tool! I was really excited to see that the latest dev version included added options to generate a BAM file. However, I'm running into an error during alignment with SMARTSEQ2 data.
…
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Hi!
I was granted an access to phs001680.v1.p1 data from dbGap - original paper here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6641984/. I downloaded all the scRNAseq (Smart-seq2) files with…
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I am trying to run velocyto (CLI) on bam files to generate loom files with spliced and unspliced information.
i am using the following cmd
``` velocyto run-smartseq2 -o OUTPUT -e *sorted.bam mm10.…
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TCR data is readily available for Maynard and Guo (Smartseq2 datasets).
For some other datasets it might be possible to reconstruct TCR information from the raw data using TRUST4. This would requi…