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cutadapt 4.2 with Python 3.10.9
Attempted to demultiplex nanopore single-end reads with combinatorial dual indexes, but it didn't work and created a file called `{name1}-{name2}.fastq.gz`
`cutadap…
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Hello!
I am using cutadapt to demultiplex my reads (v2.10 with Python 3.7.6).
Basically, I have a pair of fastq files (e.g. input_R1_001.fastq and input_R2_001.fastq) which contain sequences fro…
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**Is your feature request related to a problem? Please describe.**
Projects with many samples can produce a large amount of data in one measurement.
To analyse effects only observed in a subset of…
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As written, we currently either expect combined samples multiplexed using barcoded primers OR samples separated using Illumina indices. It turns out that sometimes people do both things, pooling barco…
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Hi @marcelm,
thank you for the development of Cutadapt.
I'm actually using the latest stable version and python 3.10.
I'm dealing with these heterogeneity spacers+primers:
Bacterial region …
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Dear hadge authors,
thanks again for your help in advance!
I am running the genetic demultiplexing pipeline for multiple samples, with a sample sheet modelled after the example you provided.
…
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Hi,
The number of "Full-Length Non-Chimeric Reads" reduced nearly half from "Full-Length Reads". Is this normal?
I started my isoseq pipeline with the raw subreads data and have run the first few …
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Need to develop methods for the pipeline to make outbound API calls during processing in order to update future LIMS/LIS systems of demultiplexing status.
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- [ ] make it clear that we are re-demultiplexing the run in the log file
- [ ] copy new samplesheet in /data/SampleSheets with filename RunID-ISODATE.csv
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### Description of the bug
When providing several samples that should be mapped to different genomes in a samplesheet, the pairing between sample (group) and genome is ignored.
Expected behaviour…