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At least in the 10x case, getting VDJ is often accompanied by gene expression data. As we are defining a format for the processed GEX data #409 , should we also provide a simple mechanism to record th…
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If config and preset windows open (background or foreground), then closing VDJ need long time to close, sometimes crash.
If windows are closed before and then you will close VDJ, VDJ closed in millis…
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With programs like Seurat and Scanpy + scirpy, we visualize the gene expression and VDJ data. I am wondering what output files from Trust4 can be used for the same purpose. Do we need to create the a …
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The answer here could simply be 'no' 😄 but as this question came up recently for me, and it is one I've seen mentioned on the `nf-core/scrna` slack, I figured I'd raise it here to get your thoughts. …
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It would be great if the tool could produce a FastQ file from the VDJ pipeline BAM files (e.g. `all_contig.bam`), including the usage of the `--bx-list` option as well.
Thanks in advance.
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Dear Dr. Li,
Firstly, I would like to express my gratitude for creating such excellent tools.
I have utilized TRUST4 to analyze my different spatial TCR data set (TRA and TRB are enriched separ…
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Hey,
I am using cellranger version 7.0 and running the `cellranger vdj` function.
The output of `cellranger vdj` function contains a folder named `outs` (as described here [https://support.10xgenomi…
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Hello,
I have been able to change the colour scheme of plots for gene expression analysis. But I am unable to customize colours in the plots for VDJ repertoire analysis (for example the bar plots …
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**Description**
When I did as the tutorial on official [tweets](https://mp.weixin.qq.com/s/hqh7DJPzLsC45LepTI8Q7Q), I met some issues as running the following codes:
`celescope vdj mkref human TR`
…
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Hi,
We recently ran TRUST4 on some 10x Genomics TCR data using the command
`trust4 -f hg38_bcrtcr.fa --ref human_IMGT+C.fa -1 input/YWI006-VDJ_S1_L001_R1_001.fastq.gz -2 input/VDJ/YWI006-VDJ_S1_L001…