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Hi,
I was trying to demultiplex 20k cells to 4 donors. But only a few cells were assigned to each donor. each donor was genotyped using Infinium Omni2.5Exome-8 v1.5.
The vcf file looks like th…
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Specifying in this step UMI, polyT, and TSO_seq :
`config_file
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### Description of feature
- [ ] MAIN::extract_csv
- [ ] MAIN::parse_flowcell_csv
- [ ] BCL_DEMULTIPLEX: :generate_fastq_meta
- [ ] BCL_DEMULTIPLEX: :readgroup_from_fastq
- [ ] BASES_DEMULTIPLE…
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Hi Stewen,
Can you share the script for rhapsody-demultiplex and rhapsody-extract-barcode?
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Dear team,
Thank you for providing the tool to demultiplex. There are 16 donors in one pool in our data. We have paired genotype to demultiplex. My input vcf contains 10w exonic SNPs. I ran Vireo …
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Hello,
I was testing out your pipeline to see if it would be compatible with how we currently run our demuxing, and ran into some issues. Here is the command:
```
nextflow run csawye01/nf-core-de…
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Need to convert the `Demultiplex_Stats.htm` table output by `bcl2fastq` to one or more .csv formatted tables for easier usage and importing elsewhere.
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https://github.com/rrwick/Porechop/blob/289d5dca4a5fc327f97b3f8cecb68ecaf1014861/porechop/porechop.py#L277
Unfortunately, the barcode (12a) breaks this syntax because the folders are labeled 12a in…
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I was wondering if there was a tool for demultiplexing scRNAseq fastqs at the level of single cell, so that I have one fastq files for each cell in my data set. This will allow me to have the proper i…
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https://github.com/moka-guys/automate_demultiplex/blob/713d75a746f59525ff3beb88e18ff5fb103c16b1/automate_demultiplex_config.py#L1377