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I have observed cases where my dual UMIs can get swapped during amplification steps in library prep, resulting in two consensus sequences which align to the same start/stop position but share the half…
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Hi,
I am using bayesian filteration of UMI, with -s in Droptag and -r in Dropest, everything seemed to be fine at the beginning, however, there was no CB recognized in Dropest and the error messages …
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**Version info**
- bcbio version (`bcbio_nextgen.py --version`): 1.2.9
- OS name and version (`lsb_release -ds`):
**To Reproduce**
Exact bcbio command you have used:
```
bcbio_nextgen.py /user…
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### Need
As a clinician I want high quality analysis, without false positive variant calls. At the moment in the UMI workflow we are not doing any quality or adapter-trimming. Not doing quality-trimm…
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Hi, I'm getting an error in processing 10X data
~/./sircel/sircel/sircel --10xgenomics \
--barcodes R1.fastq.gz \
--umis I1.fastq.gz \
--reads R2.fastq.gz \
--output_dir ~/10x_out --kallisto_i…
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### Is there an existing issue for this?
- [X] I have searched the existing issues
### Community Note
* Please vote on this issue by adding a :thumbsup: [reaction](https://blog.github.com/2016-…
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Hello,
is there a way to import a dataset that is saved in .h5ad or in .loom format into metacell?
Thanks!
Alessandra
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Hi! After running `group` on a sorted bamfile of roughly 3.4 million reads, I noticed that only half (~1.6 million reads) were actually given UG tags.
I checked this by running `samtools view -d U…
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Hi AMULET team,
I have a 10X multiome kit dataset and trying to run AMULET on the ATAC data.
The fragments input file is the same, but the singlecell.csv is no longer available as CellRanger outpu…
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Hi everyone,
Is there a way to feed pre-transformed files into Alevin? We've been using Valentine's nice umis repository https://github.com/vals/umis as our preprocessing step to put sample, cell a…
roryk updated
5 years ago