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What maxExpectedError combination provided by Figaro is recommended for Dada2? Shoud I use the best [2, 3] result provided by Figaro or do you recommend to stick with the best [2, 2] result as recomme…
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Thanks for your help. This issue could be cancelled if it's fine with you.
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Hello Developer,
I'm trying to use your tool to perform assembling from MinION run of 1 single amplicon of 7441 bp . When I launch the program it says:"Expected read coverage is 496301, the assembly …
BioRB updated
4 years ago
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HI, I am trying to make the database from source using the make_databses.pl. But, I am confused about why there is a need to download the preformatted database file as shown in the make _databses.pl …
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Dear Kristoffer,
We amplified two markers (the nuclear ribosomal cistron ~6000 bp and a low copy nuclear gene ~2500 bp) for 12 samples. Then we combined both markers for each sample and barcoded th…
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I tried to find best-practice instructions for dealing with overlapping primer pairs like the ones found in the [Artic V3 primer scheme for SARS-CoV-2](https://github.com/artic-network/artic-ncov2019/…
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Hi Ben,
I'm following the dada2 ITS workflow with fungal ITS2 amplicon sequencing data with 2x300 bp reads from an Illumina MiSeq platform.
According to the sequencing firm, my first sample conta…
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Need to swap cutadapt parsing for trim galore and ivar trim. Also need to change the directory where Fastqc files are found post-trimming. May want to run fastqc after ivar trim instead.
nknox updated
4 years ago
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I'm a bioinformatician with a research group studying - broadly - microbial ecology. We're doing lots of metabarcoding experiments, so in 2018 I created two custom taxonomy assignment training sets to…
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Hello,
I have variable length barcode and in my case I trimmed all my sequences to the maximum length (from my longest barcode), so I have for smallest barcoded sequences a lost of a few true biolog…