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I want to use bcbio to process TruSeq Custom Amplicon (TSCA) data. However, I notice the performance of bcbio's variant2 workflow is not great (comparison to MiSeq reporter workflow below).
I comp…
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Dear All,
I am trying nf-core amplicon pipeline for my analysis. I have reads from two different sequencing run. my input files looks like as follows:
data
|-run1
| |-01_TM48_F.fastq.gz
| …
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Let me know if this is a question better asked in another forum. I'm using mothur to do some QC on data from a highly multiplexed amplicon sequencing panel (~135 primer pairs x 48 samples). I'm having…
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Add "Highly targeted resequencing", "Targeted next-generation sequencing panels", "Amplicon panels", "Panels", "Amplicon-based sequencing" as narrowSynonym of "Sequencing" ... more likely making "Res…
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I recently read your paper titled “High-throughput amplicon sequencing of the full-length 16S rRNA gene with single-nucleotide resolution. Nucleic Acids Research, 2019.” I am currently applying your d…
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when I use vsearch for amplicon sequencing data analysis, I have installes vsearch
when I use it, something wrong happended:
`ubuntu@ip-172-31-14-112:~/LC$ time vsearch ‐‐usearch_global seq18s-A…
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Hi,
I have read the FAQ and saw this question is addressed but I do not know how to proceed.
I have 742 paired end samples from Ilumnina HiSeq runs that I demultiplexed. Barcodes and primers (51…
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Hi all, I am trying to analyse with DADA2 some PE reads downloaded from SRA but when I merge them after Dada2 pipeline I get very low output (range 0-10). Is there an additional step that I am missing…
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I started working on this
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Hi I am new to DADA2 and am trying to learn how to convert sequencing data into OTU tables. I have a WGS read level data where I have fastq paired end data files for each sample. Can I process this d…