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extracting the 16S rRNA gene and doing an OTU clustering will illustrate the diversity captured with targeted amplicon sequencing
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csv, tsv, text, whatever
Raised in amplicon walkthrough 07/30/2018
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Hello,
I see that most of the data resources provided for the GIAB samples are wither WGS or WES (similar). I was wondering if there is any source for targeted data (for eg: hybrid capture or ampli…
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Hi Heng,
Always interested to test out new software that you put out. I am doing a lot of targeted resequencing with Illumina TruSight Amplicon data of tumour-only samples. I have been looking for so…
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Hi,
Thanks for creating and maintaining this amazing fieldsbioinformatics.
I stumbled across this silent bug when running a new primer scheme for MPXV (spiked in yale scheme). The `primer.bed` f…
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Dear Jennifer,
while installing q2-ghost-tree to the qiime2 version 2022.8, I got the error message
NameError: Duplicate view registration ('AlignedRNAFASTAFormat') defined in plugins: 'ghost-tree' …
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[https://xyz1396.github.io/2019/06/29/upload-16s-amplicon-sequencing-raw-data-to-NCBI/](url)
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I am trying to run velveth on my paired files but facing the following error:
[0.000000] Velvet can't handle k-mers as long as 33! We'll stick to 31 if you don't mind.
[0.024794] Reading FastA fil…
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Accumulating a bibliography of papers describing oligotypes and amplicon and exact sequence variants
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Hi,
My sequencing data is amplicon sequencing that some regions got excessive coverage. I wonder if I can set a maxi coverage in Pisces.
Thank you!