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I run cojac on wastewater samples which are sequenced using NimagenV3 primer amplicons. It worked well for most variant profile however I encountered this error while using a profile which has co-occu…
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When providing a target fasta longer (e.g., 1kb) than the specified amplicon (250 nt), the histogram PDF appears to calculate median mutation rate incorrectly (specifically, deflates the mutation rate…
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Hi,
I had a run with primer designer with this parameters:
Strangely, in the result, the amplicon is built over the starting point of the region. Which sequence would the pipeline take in su…
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Develop a workflow that better supports the creation of additional amplicon target descriptions. At a minimum format unassigned for blast searching or integrate searching against a reference genome.
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I am trying to use DESeq2 for amplicon data analysis, but I am getting some problem.
Details of the analysis:
here is the summary of data,
I do have soil, root, and shoot sample collected f…
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### Ask away!
is there a schedule for making downstream workflows compatiable and up to date with the latest basecaller?
thanks
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I have encountered a mutation that consistently arises in an amplicon overlap region. However one amplicon has coverage exceeding 300x whereas the other has coverage
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The command should run Crispresso and create the outputs of the Crispresso batch file, however it is giving out a numpy error instead. @shayanhoss
**CRISPResso command to reproduce the behavior:**…
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### Description of feature
Hi there - I'm trying to use ampliseq for 12S amplicon data and running into issues adding our own custom database b/c of incompatible formatting. It would be great for amp…