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I've been helping a friend work through using DADA2 with a project that was sequenced across two different MiSeq runs. An interesting aspect of his project is that nearly all samples from the first ru…
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Hi there,
congrats on this amazing tool! I was wondering whether you have had the chance of (or planning to) evaluating DADA2 on T-cell/B-cell receptor data. Antigen receptor amplicons are conceptu…
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hello - we are running analyze shotgun w/ MiXCR 3. this pipeline appears to always run export; however, the results are not quite what I expect. it outputs separate text files for each of: ALL, IGH,…
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Hello,
I am currently working on a genotyping project that involves the use of highly variable gene markers. We used the Nextera kit for the library preparation prior to illumina sequencing in pair…
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Recently our lab conducted an experiment where we isolated strains of marine bacteria from seawater inoculum. We sequenced these cultures, a sub-sample of the original seawater inoculum, and additiona…
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Issue #38 by @dutchscientist
https://cge.cbs.dtu.dk/services/SerotypeFinder/
@dutchscientist do you have the URL for the amplicon sequences?
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Hi Ben,
I have a question regarding why I might be loosing so many reads from the Filtering to dada_f and dada_r step. The samples are 2x250bp Illumina sequencing V4. In my pipeline, the parameter…
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I'd like to run the whole test.sh script on my own data set. Until r_import_data.py everything seems ok but there I got the following error message:
> r_import_data.py --biomfile results/06-affili…
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I am trying to mutant a gene with two target sequences. From my preliminary data, I found there some mutations induced by CRISPR/Cas9 have indels at both target sites, but this software can only produ…
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Hi,
I am trying to use FALCON to run something similar to HGAP for **RSII data** (since the version of SMRT Link that I have access to is version 8.0, and not compatible with RS II subreads).
I …