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**Description**
DPL-075 As R&D lead (Scott G) I would like new LCM (low-input) combined DNA- & RNA-seq pipeline which is an expansion of the current LCM DNA pipeline
**Who the primary contacts a…
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Hello vg team
It is amazing the work you are doing.
I am relatively new to using vg and I would appreciate a little help with my question please.
I want to download an already constructed human pa…
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Hello! I'm trying to run the pipeline with the singularity flag, but I get the following error (anonymized for brevity)
```
[myuser@login001 ~]$ caper run /home/myuser/encodedcc/rna-seq-pipeline:1.2…
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I am attempting to use the prokseq-v2.0 pipeline to evaluate some data obtained by directly sequencing RNA using an nanopore device ( ONT MinION). I can test-run the pipeline using the provided data, …
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### Description of the bug
I am running `smRNAseq`on an HPC. My samples were prepared using the Nextflex library. The run was successful, please look at the code below, but the 4 bases from the 3 a…
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Experiment Type:
RNA-Seq
Sequencing of total cellular RNA
Workflow Management:
Bash/SLURM
Scripting and job scheduling
Software Stack:
FastQC
MultiQC
STAR
RSEM
samtools
DESeq2
What …
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Hi
I was trying MGCount on Plasmodium Falciparum BAM files obtained from cellranger (10X 3' chemistry) and I get the following error. Can you suggest what's wrong here?
Python 3.11.5
MGcount R…
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I have tried running both the run_ORQAS.sh script and running the pipeline step by step. I have tried using my ownrnaseq and riboseq data and the sample data. I keep getting the same error.
termin…
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Hey,
Wanted to run this pipeline with comparable combinatorial barcoding snRNA-seq (Sci-RNA-Seq3) but realized an input file is missing.
Script: Section_1_processing.R - line 17:
"mouse_gene…
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The RNA-Seq pipeline will stop using `factors` in its next release.
For `factorValueObjects`, it's been replaced by simply `factorValues`.
@oganm will this affect the R or Python packages?