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Test run on human_pancreas hvgs = 0
```
human_pancreas_norm_scvi_hvg0_err.txt
Traceback (most recent call last):
File "/home/icb/daniel.strobl/Benchmarking_data_integration/scripts/runIntegratio…
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@cusanovich , What is the structure of the barcode? and the format of fastq file?
And `sc_atac_10bpbarcode_split.py` script failed to process the ATAC-seq fastq files.
Here are the errors, `barc…
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hello, Thanks for providing such useful tools for sc-RNA seq data and sc_ATAC seq data。However, when i reading the tutorial about "PBMC scATAC-seq Vignette ",i want to input the annotaioned scRNA-seq …
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Hi all,
I was trying to get snakepipes running on an Ubuntu 16.04, following the "Setting up snakePipes" from your readthedocs page, but when creating the environments I get the error(s):
```
…
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Example: http://artyomovlab.wustl.edu/publications/supp_materials/4Oleg/2019_sc_ATAC_seq_gxfer1_39174753087306/session2.yaml
olegs updated
5 years ago
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@danielStrobl @mumichae It looks like we just keep going until we have 4k HVGs in the intersection in this function.
https://github.com/theislab/Benchmarking_data_integration/blob/81aa23057223970e75c…
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**Describe the bug**
Incorrect computations of NFR and "Presence of NFR peak', 'Presence of Mono-Nuc peak','Presence of Di-Nuc peak'.
Details description
The source code for defining NFR is at …
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Hello,
I am running the first part of the pipeline as described in the ReadMe:
python sc_atac_fastq2bam.py -R1 SRR5837698_1.fastq.gz -R2 SRR5837698_2.fastq.gz -O pre.processing -P scATAC.Repro…
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**Describe the bug**
Last step ATAQC get terminated and failed to generate QC report. The only file I see in this step's output directory is only regarding the gc report(trim.merged_gcPlot.pdf etc.) …
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olegs updated
5 years ago