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Hi,
Would it be possible for demuxmix to model the HTO data together with VDJ data, rather than GEX data, where
for VDJ data there are RNA (UMI) counts for the number of times 2 chains (i.e. BCR…
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Hello,
Is there a way to calculate the ram requirement for the program? I run the program on a cluster. The jobs are killed because of high memory usage. E.g. my lastest job exceeded 256 GB RAM usa…
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I'm using cutadapt 4.1 with Python 3.10.6 through conda.
I'm trying to demultiplex a dual indexed library with inline barcodes where the first 8 bp of each read are a unique barcode.
My command…
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Hi - Thanks so much for this pipeline!
I am getting the same issue as you were getting with vartrix that you posted about here: https://github.com/wheaton5/souporcell/issues/126. I am using the code…
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I would very much like to use MetONTIME for long read sequences and to proceed with 16S analysis.
However, when I run Launch_MinION_mobile_lab.sh, I get the following error and it stops.
In MinION…
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I am trying to read multiple 10X libraries using the `read10X()` function. The libraries were run in two batches. Batch 1 was multiplexed with 4 samples per library (B0301 - B0304), whereas batch 2 wa…
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Out of curiosity, have boutier's changes/features been integrated into the mainline repo? If not, are there any plans to?
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Hello,
I am analysing a 10x scRNA-seq dataset where 6 cell populations were multiplexed by antibody-based cell hashing (with Totalseq-B antibodies). I demultiplexed the dataset using either `HTODem…
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Dear all,
I am trying to analyze a public [dataset](https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA407224&o=acc_s%3Aa), created with the C1-STRT protocol, using umi_tools in order to replicate…
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In all of our experiments Minions cannot keep up with live-basecalling and demultiplexing in realtime. When this happens, the software stops live basecalling and demultiplexing and sends all the read…