-
Per the latest version, cutadapt can now demultiplex samples and remove adapters at the same time, with multithreading https://cutadapt.readthedocs.io/en/stable/guide.html#demultiplexing. It appears t…
-
Hi Dorado team,
I have performed dorado duplex calls, then from the resulting BAM file, I have used the below command to only compile a bam file consisting of duplex calls:
samtools view recovered…
-
### Description of feature
The early steps in the pipeline run multiple samples in parallel (e.g., if there is 10 samples, fastqc gets run 10 times). This is the normal way of doing things in nf-core…
-
Hi,
It will be great if the `--emit-summary` option for `dorado demux` also exists with `dorado basecaller`. With this new feature, it will be possible to perform basecalling, demultiplexing and cr…
-
## Description
There could be a current bug where flowcells have issues assigning and de-assigning the status `ondisk` in statusdb. There have been several instances in production where analyses co…
-
The functions related to receiving UDP data (hasPendingUDPBytes, waitForUDPResponse, socketReceiveBytes) do not have a socket argument. This design looks a bit strange to me. Why did you choose it? Wo…
-
I am attempting to convert DIA files from a Fusion Lumos to mzML with MSConvert 3.0.23208-1321c92. When I attempt to convert, I get the error:
"Error writing run 1: SpectrumToIndices() Number of de…
-
For the RNA samples I am running, demultiplexing gives significantly different results. GPU mode results has a lot more unknown assignments and very small number of bc3 barcoded reads. Meanwhile CPU …
-
Hi,
We're running the following Reporter commands to obtain a report containing the individual sample ratios using a TMT 11-plex pool
`java -cp Reporter-0.12.0/Reporter-0.12.0.jar eu.isas.report…
-
It runs well in the non-basecalling, non-demultiplexing, non-alignment pipeline. However, it not runs well in the non-basecalling, non-demultiplexing pipeline. The test dataset is from nf-core/t…