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Hello team,
We recently processed some T-cells samples with the Takara SMART-Seq Human TCR (with UMIs).
We used the command "run-trust4 --barcodeLevel molecule -f $Genome/hg38_bcrtcr.fa --ref $…
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Your algorithm appears to catch all cases that I could think of, good job!
Good idea to reverse complement the UMI list at the beginning of your script. I am going to incorporate that into my scri…
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Dear all,
I've been trying to use `fgbio CorrectUmis` to process some data from Illumina's TSO500, but they use a mixture of 6bp and 7bp UMIs.
Since `bcl2fastq` needs a fixed length UMI, we've…
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Hi authors!
I have some single-cell ATAC seq data from 10X on which I would like to use demuxlet, however there is no UMI barcode in ATAC seq results. Is there a way to specify that there is no UM…
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UMIs are mostly used to track single molecules and enables us to distinguish them amongst the different reads we got from an experiment. With them, we are able to not mark as duplicates identical read…
Poshi updated
3 months ago
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## Feature request
### Tool(s) or class(es) involved
PathSeq
### Description
I would like the PathSeq scoring approach to be able to consider UMIs such as those used in scRNA sequencing experi…
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Everything looked to be running fine:
```
!CITE-seq-Count \
-R1 $Hash_R1 \
-R2 $Hash_R2 \
-t feature_barcode_onlist.csv \
-cbf 1 -cbl 16 \
-umif 17 -umil 28 \
-wl 737K-august-2016.txt \
-T 8 …
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- [ ] Add common visualization code to verify/determine thresholds being used on various QC metrics. Should be a general plotting function. Name and module:`sciduck.pl.qc_metrics()`?
- [ ] Include in…
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Hello,
I encountered the following issue while running the run_calibration_check() function:
```
sceptre_object
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When demultiplexed with a read structure indicating presence of UMIs (including `M`; ex. `146T8B9M8B146T` for a 9bp UMI), the resulting bam files include per-read UMI sequences via the [RX tag](https:…