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From Slack:
> Joel Welling: For UCSD sc-ATAC-seq, is there a plan for how you’ll work with the current organization of files on Globus? The problem is that they’ve created directories per sample on g…
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Hi,
Is it possible to run integrated analysis similar to https://satijalab.org/seurat/v3.0/immune_alignment.html on scATAC seq data? Please see my attempt below with the error produced. I followed …
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**Where is the problematic documentation?**
The explanation for loading in bamFiles from combinatorial indexing-type snATAC-seq files (e.g. sc-THS-seq from Preissl et al 2018, Lake et al 2017).
1…
badoi updated
4 years ago
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Hello!
I am trying to run the mRNAseq pipeline on the provided test data, but I can't seem to be able to get past the following error. Unfortunately the STAR .log is empty.
Error in rule STAR:
…
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Hi, thanks for providing such great tools.
I followed the tutorial. installed using
`conda create -n snakePipes -c mpi-ie -c conda-forge -c bioconda snakePipes==2.1.1`
`conda activate snakePipe…
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What exactly is the difference between MACS2 and this MACS3 project?
What specifically is trying to be aimed by MACS3?
Could not find a clear explanation of this searching through the "Issues"…
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Clarify exactly what the name should be.
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Hi Tim,
I'm trying to identify the motif difference between patients and healthy controls in CD4+ cells by using RunChromvar. My code is attached below.
It is strange that although the a…
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Hi,
Pipeline fails immediately, giving following error:
[error] Failed to instantiate Cromwell System. Shutting down Cromwell.
java.sql.SQLTransientConnectionException: db - Connection is not …
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Hi,
My understanding is there are only two states of a chromatin region, either open or closed (1 or 0) in most areas. The different levels of read counts might largely reflect amplification bias rat…