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Hello,
I have 2 10X Genomics datasets (BCR and GEX). What are the appropriate parameters setting for TRUST4?
I'm using
f"run-trust4 -1 {f1} -2 {f2} --barcode {f1} --UMI {f1} --readFormat bc:0:15,…
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Hi! I'm brand new to using immunarch and am preparing to use it to analyze some cellranger vdj data from 10x genomics. I was a little confused in the "Loading 10x Genomics Data" vignette, because orig…
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### Description of the bug
```bash
nextflow run main.nf \
-ansi-log false \
-profile docker,gcp \
-work-dir gs://path/to/bucket/scrnaseq/work \
--input samples.csv \
--protocol…
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Hi,
For SC5P chemistry, I should be able to define 0,0,16:0,16,26:0,26,0 for the 1st read and 1,0,1:1,0,1:1,0,0 for the 2nd read in -x parameter.
Can this be done?
Best
Pasi
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Dear Peter,
We were hoping that hapCUT2 would allow us to skip LongRanger to phase variants. However, we are running into some issues, and I would like to check back with you regarding some questio…
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Hello, Dr. He. Sorry to bother you again.
I already knew that SEVtras would work with single cell RNA sequencing data produced by the 10x genomics chromium , which is based on droplet sequencing, but…
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Hi,
The Xenium are imaging-based ST technology so that the Xenium dataset's spatial coordinates are not supposed to be grid.
Why does the TENX99 dataset have the grid coordinates.
I check the …
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Dear Dev,
I am new user of TRUST4 on single cell TCR seq analysis, regardless, TCR seq could be successfully obtained using bulk RNAseq data.
I wonder, with my 3' 10x genomics GEX data (I have b…
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We are looking to have more specific ontology terms for Visium, as 10x has come out with variations of the assay. Here is some documentation regarding the version of the slide in the slide serial numb…
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Hi there, thank you for this amazing tool. My team as been using it a lot (see issue #265) but when I try to reproduce the analysis I came up with a few questions.
I did 10x genomics kit 5` GEX an…