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### Objective: As a user with a pipette, I would like the DCP to process 10x v2 and v3 single-nuclei sequencing data (snRNA-seq) so that I can submit such data to the DCP and view the results in the d…
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Hi,
I tried your pipeline with default parameters with long reads data (pacbio hq isoforms mapped with gmap) and NGS reads. A lot of my isoseq transcripts/isoforms (exons) were filtered out. See th…
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Hello, PROT provides useful pipeline to handle multiple RNA-seq data sets.
And the new references are published, like hg38, mm10. etc.
So, could you provide the annotation of these files?
Thanks!
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For some applications, such as protein-RNA complexes, I'd like to pair sequences by a custom method- and input already paired seqs (2 alignments where sequence X in ali 1 is paired with sequence X in …
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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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read_json almost never work for me. Here is for instance a json that is totally valid but breaks read_json
```
{
"id" : "GSM1698568",
"gse" : [
"GSE69360"
],
"title" : "Biochain_Adu…
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**I was having issue when the trinity has to make the final fasta file, trinity has ran for almost 25 days before I have reached to this .**
**Trinity version: 2.13.2**
**Command Used**
/share…
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Experiment Type:
RNA-Seq
Sequencing of total cellular RNA
Workflow Management:
Workflow Management:
Bash/SLURM
Scripting and job scheduling
Software Stack:
FastQC
MultiQC
STAR
RSEM
sam…
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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…