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Based on the guide of generic-amplicon preset, the reads are constructed as follows.
The read outputs that I am trying to process through MiXCR, however, looks like this. R2 has the UMI sequence…
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We (@boospooky and I) are trying to better understand the meaning of the QUAL scores that are calculated by nanopolish. A [while back](https://github.com/jts/nanopolish/issues/263) @jts explained that…
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**Describe the bug**
Running CRISPRessoPooled, results in failure message.
`Unable to find matches for header values. Using the default header values and order. ERROR: Incorrect number of columns …
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Hello, when looking at the mixcr report, I find two TCR repertoires with exactly identical CDR3 amino acid sequences and 1 mismatch in CDR3 nt sequences. These two occurrences have equal V and J segme…
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Hi,
I am trying to use a miXCR pipeline published in a STAR protocols paper: [Localization of T cell clonotypes using the Visium spatial transcriptomics platform](https://www.sciencedirect.com/scie…
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Hi,
We are trying to detect chimeras in some nanopore 16s reads. Although we already know that there are some chimeras in our reads, we are not able to detect them using the parameters from the yac…
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Hi, I have an issue in removeBimeraDenovo function. I have 185 samples and 373744 reads. When I run removaebimeradenovo system crashes after couple of hours of running without any error, and the R se…
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Hi, I have notice a problem on sequencing reads produced by amplicon sequencing (marker COI-5P). Indeed, in some cases, with samples usually having thousands of reads, NGSpeciesID outputs multiple (2 …
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Hello,
I am running MIXCR with preset generic-amplicon-with-umi and generic-amplicon.
Since our wet-lab protocol supports 7bp UMI, there seems to be a high level of duplicate reads that gets fil…
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It was observed that the resource requests for the processing pipeline, with an amplicon sequencing run, are very large. The amount of resources used is small compared to the request. What I suspect i…