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Hi, thanks so much for developing this great tool. I just run a 10x Genomics scRNA sequencing on a pool of hashtag multiplexed sample. I tried to use the cmd below to generate the cell-hashtag count m…
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### Ask away!
To whom it may concern,
I am a user of wf-single-cell and I have some questions regarding the internal workings of the pipeline, specifically concerning the barcode and UMI correctio…
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Hi there,
for single cell bam files that I am processing in the same isoquant command, how does Isoquant deal with cellular barcode found across multiple bam files? Does it aggregate this informati…
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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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# tl;dr
- `salmon alevin` returns an error if the cell barcode length is > 31 base pairs
- This blocks me from using `salmon alevin` for a novel scRNA-seq chemistry that has a 34 base pair cell barc…
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A large amount of specimen labels that were ordered for DaSSCo were not reserved in Specify and are already in use by others (#151 ).
Out of the 250.000 numbers that were printed but not reserved, the…
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Hello,
I tried the SoloTE on a published dataset but what I am observing is that after running the SoloTE on bam files and then making the Seurat object I am observing quite a variability in the to…
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## Description
When `tissue_positions.csv` rather than `tissue_positions_list.csv` is in the spatial directory for a Visium dataset, the resulting AnnData object has:
- NaN in adata.obs array_row, a…
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Hi,
i run the subset-bam using the following command,
./subset-bam_linux --bam SCAF654_1-1.bam --cell-barcodes SCAF654_1-1_barcodes.csv --out-bam SCAF654_1-1_bam
The run takes 14hrs without mis…
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fastplong -w 128 -Q -i ont.fq.gz -o fastplong.fq.gz
Trying to detect adapter sequence at read start
Detected: TGTACTTCGTTCAGTTACGTATTGCT
Trying to detect adapter sequence at read end
Found possib…