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Hi zUMIs folks,
I am trying to troubleshoot a situation that I have ran into and would like some help.
I apologize for my long entry in advance.
Input conditions (here is what I have at hand)
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Hi,
I have tried to run STARsolo on smartseq2 data (~1000 cells) using your starsolo script. The run completes but doesn't produce any files in the output folder. When I ran the script on one cell, I…
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Dear Community,
I am trying to run STARsolo on my SmartSeq2 samples. I am using following command
`STAR --runThreadN 16 --genomeDir /home/jupyter/HumanGenomes/ --readFilesCommand zcat --readFil…
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Hi developers,
The current default usage of `kb count` is to generate a gene-level UMI count matrix. I wonder if it is possible to get the UMI count for each specific isoform using kb? Thank you if y…
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### Project short name:
MegakaryocyteDevelopment
### Primary Wrangler:
Ida
### Secondary Wrangler:
### Associated files
* Google Drive: [MegakaryocyteDevelopment](https://drive.google.com/drive/…
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Current status of datasets:
https://docs.google.com/document/d/1a8uu0-GclIa9yy2Hs_AkoSJnMEOHLZkQdmCzwWlueoQ/edit#
Test-cases suggested by Francesca:
1. Mouse data: it would be a completely new ap…
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Currently workflow imports of WDL documents are not translated.
A workflow using imports can be found here: https://github.com/broadinstitute/warp/blob/b3f5c898d1b535aaca8dc9e9f4223697a7a0a9a9/pipel…
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**Describe the bug**
The graph validator raises the smartseq2_has_2-3_files error even if the sequencing is single-ended
**To Reproduce**
Steps to reproduce the behavior:
1. Upload a submission …
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**Short name**
HumanThymicDevelopment
**Primary Wrangler:**
Marion
**Secondary Wrangler:**
Ray
Google Drive:
https://drive.google.com/drive/folders/1-cPgACNjW4TXe9mnLQuEZE7uEHX-7aEZ?usp=sharing
…
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Hi,
Francesca pointed me towards a chapter we did not really cover yet with the simulator, comparing the simulated expression counts with true bulk RNAseq counts. Basically if the simulations even …