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I'm trying understand the tools utilisation for grouping the UMI and building the consensus, however what may be the reference file in the context for VAULT. I went through the example files, quite di…
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I just came across the preprint and got curious to try out burst.
I need to assigning the taxonomy for Illumina short-reads (MiSeq, up to ~450bp) from an amplicon sequencing run (COI & 16S). Are t…
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I saw in #7 that for amplicon-awared variant calling, the BED file need to have 8 columns storing both the primer and insert positions. However, the BED file that comes with the manufacturer's target…
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Hi,
Thanks for the tutorial!
I would like to determine the co-occurrence between two different composition from the same samples (I used two different amplicon sequencing approach from the same sa…
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Hi Bram,
I am using RTCR to identify the TCR repertoire from amplicon sequencing. I have some more question abouts the output result.
1) how can get the mapping rate for the fastq reads (MiSeq, …
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Hi,
We recently implemented masking using this table. We realised that certain sites might only require masking when using a particular primer set as we are seeing sites for lineage defining mutati…
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"Whole-genome sequencing and targeted amplicon capture" says:
> "Do not mark duplicates in the BAM files for samples sequenced by this method"
However, in the BAM file preparation, it is writt…
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Dear Jennifer
By default, bracken set the cut off of reads number 0 as the presence of a taxon in the sample. However, it is quite obvious with our data that if set 0, tremendous false positive spe…
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Can we use Snippy for phylogenetic tree construction for COVID-19 from Fastq reads. If not, Can you suggest some tool to work with fastq reads
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I tried the program on PacBio hifi reads, which were for amplicon sequencing of some plant DNA samples, barcoded on both ends. The reason is that LIMA generated very simple report missing a lot of inf…