-
Hi,
I was trying to get a list of final, filtered cell barcodes. I downloaded the MS_CSF.h5ad file linked, but when opening it in R, the column names are just 1,2,3,4... instead of the cell barcodes.…
-
The command `umi_tools extract` results in read names being suffixed with the pattern `_[cell barcode]_[UMI]`. See [the docs here for an example](https://umi-tools.readthedocs.io/en/latest/regex.html#…
-
"Major note if there are duplicate barcodes (if a cell has both Ig and TCR), the immune receptor information will not be added. It might be worth checking cluster identities and removing incongruent b…
-
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…
-
Hello -
In some workflows that could use umi-tools, we already have an explicit whitelist of the corrected cell barcodes. There is still a need to identify the non-error-corrected cell barcodes.
…
-
Hi @hxj5 , I have a question regarding 10X 5' scRNA-seq data.
For 5' sequencing, the read containing cell barcode and UMI contains part of the transcript https://kb.10xgenomics.com/hc/en-us/article…
-
Hi Dr. Wang,
I have just read your paper "A mouse model with high clonal barcode diversity for joint lineage,
transcriptomic, and epigenomic profifiling in single cells" and fairly interested in the…
-
I read in Lior's preprint X thread that splitcode would work well with long-reads, do you have any example of how to implement it for this case?
I would like to test it to demultiplex single-cell lo…
-
### Ask away!
Hi! I have a quick question. I've read several post that people have their processes stuck specifically at stringtie step for large input, and I've encounter the same. Specifically, it …
-
### Is your feature related to a problem?
Some reads are inevitably thrown out due to lack of barcode, basecalling errors/below Qscore threshold, etc.
### Describe the solution you'd like
If you ha…