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Hello,
I found an issue where the barcoding_summary.txt generated by `dorado demux` is not working properly while using the --no-classify. I'm running the barcoding from the `dorado basecaller` ste…
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Dear Rongxin,
can I add additional metadata to 1) single barcodes/cells or 2)even only to whole experiments during "createSnap"?
Concerning 1 I want to add protein-expression values and then visu…
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Hi team, thank you for developing this great tool. I tried running it but ran into a weird error where it says: fail to write samples to '/hpcfs/groups/phoenix-hpc-pololab/Mike_prostate_SNP_trail/outp…
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Hi,
My input bam files come from a 10X Chromium experiment and have entries with format
GTTCCTCCAAGTCGATGGCACCTCCCTCCCTCTCAACCACTTGAG DADBCHII?FGE?DCGGEG1@
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Hi,
thanks for devoloping this tool!
I'm trying to run citecount with 10xGenomics 5kPBMC public data as a test for the tool. in principle, it should work as i have specified a trim of 10. I also u…
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Hi,
Thanks for developing a subset-bam software. I would like to split the BAM file (from cell ranger) for each individual cell barcode, which is provided in the filtered_feature matrix folder (bar…
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**Goal**
Development of a stand-alone fastq validation tool.
A flexible tool that can be applied to different single-cell technology types to check for the expected cell barcode.
It should also r…
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Hello,
After running your software, I noticed that some beads were classified as originating from the same cell. Could you please explain how this determination is made? Specifically, I'm curious a…
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I ran MIXCR on single cell data TCR data. After exportClones , I saw some rows with the same cell barcodes (tagValueCELL column) but different cloneId. This means one cell belongs to different clonoty…
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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…