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Hi,
I'm trying to run the velocyto on the bam file from cellranger V3.
After running the CLI code, I can generate the cellsorted bam file, but cannot generate the loom file. Could you help to check …
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Hello,
I used the following commond generating the genes/TEs expression matrix and imported into scanpy to cluster, visualization.
But, the gene expression generated from scTE were largely not con…
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**Snakemake version**
snakemake version 8.12.0
**Describe the bug**
I can run my snakemakefile interactively without any issue ```salloc --nodes=1 --partition=acompile --ntasks=1 --time=01:00:…
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Hi @HeQSun ,
Very impressive pipeline!
I'm interested in the crossover identification step for the scCNV-sequenced nuclei. I have downloaded the aligned bam for the two 10xCNV libraries (thanks…
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I hope this message finds you well. I am currently encountering some difficulties while running a program, and I would greatly appreciate your assistance in resolving these issues.
> library(SingCe…
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Hi, Rongxin,
SnapATAC is fast and has good performance. I really like it.
when I used snapATAC on my own data from 10X, I found the barcodes in bam file after 'snaptools align-paired-end ' were…
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I am analyzing data similar to 10X format(seekone DD_5) using TRUST4 , which is single-cell VDJ data with barcodes and UMI. The results of the TRUST4 analysis include both airr and barcode_airr tsv re…
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Many thanks to @edg1983 and @ewels for the cellranger module https://github.com/ewels/MultiQC/pull/1821. Cellranger count is most commonly ran with GEX data only, but can also support feature barcode …
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Would it be possible to add an option to run VDJ analysis using the IMGT database as the reference (as opposed to vdj_GRCh38_alts_ensembl-5.0.0, the current reference)? 10X provides a build script fo…
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Hi, I would like to ask, for the h5ad file input by cellbender, should I use the raw data or the filtered data?
Thank you for your time, thank you!