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We use merged platform because adding RNA-Seq data require that the same platform is used for all the samples. This is unnecessary because ultimately these platforms get replaced by a generic expressi…
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### Is there an existing issue for this?
- [X] I have searched the existing issues
### Description of the Bug/Issue
I'm working on validating this pipeline on samples sequenced on both Illumina and…
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### Description of the bug
I’ve been testing ampliseq on some Element Biosciences data using standard Illumina settings and discovered an interesting issue where DADA2_ERR fails with error that looks…
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Hi,
I have been trying to analyze my sequencing data that come from an AVITI platform instead of Illumina. The FASTQ quality score are higher than 41, which results in an error when I run the itsxp…
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Hello again!
I want to process the sequencing data obtained by Croce _et al_ in **"Phage display profiling of CDR3β loops enables machine learning predictions of NY-ESO-1 specific TCRs"** with TRUS…
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### Description of the bug
Hi, I ran the command "nextflow run xiaoli-dong/pathogenseq -r 5a4a403 --input samplesheet.csv -profile docker --outdir results --platform illumina --skip_illumina_dehost …
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@hyanwong noticed that some sequences have the same GenBank accession in the latest Viridian trees.
For example, the following GenBank accessions have multiple sequences associated with them (the l…
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Currently, `ILLUMINA` is hardcoded in as the platform in the bam header. With more platforms being used in the genomics core (particularly `ELEMENT` and `ONT`), we should provide flexibility in config…
kew24 updated
1 month ago
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The field will be used to specify the sequencing platform applicable for the application.
It will be located next to the field "prep category".
"Platform" needs a drop down list with the following…
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hi
I want to use pgcgap to construct a whole genome phylogenetic tree of 120 strains. I used pgcgap to read in the genome file, but it seems that pgcgap can only read files of the same format. Howeve…