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Unexpected amplicon sizes in MinION MK1D sequencing run (16S, 18S, 28S, ITS)
Hi everyone! We are using a MinION MK1D sequencer with its corresponding software for basecalling, and EPI2ME for data interpretation. We performed an... -
Small amplicon library sequencing
Hello all,
I have had several troubleshooting attempts at sequencing a low-diversity, small amplicon library on a NextSeq2000 using P1 50...Last edited by CitizenSnips; 09-08-2025, 06:16 AM. -
Improved Targeted Sequencing: A Comprehensive Guide to Amplicon Sequencing
Amplicon sequencing is a targeted approach that allows researchers to investigate specific regions of the genome. This technique is routinely used in applications such as variant identification, clinical research, and infectious disease surveillance. The amplicon sequencing process begins by designing primers that flank the regions of interest. The DNA sequences are then amplified through PCR (typically multiplex PCR) to produce amplicons complementary to the targets.... -
quality score issues
Hi all,
i am wondering what are possible causes of low Q30 scores, apart from overclustering?
I am working with amplicon... -
Understanding ASV data
Hi, I am new to bioinformatics and do not have much biology knowledge. I need to use some ASV (amplicon sequence variant) data, and I do not know where... -
16S & 18S Deep Sequencing Request(s)
Hello,
We've done 16S/18S/ITS/amplicon sequencing for years, with good results - sometimes excellent (library dependent) - for both internal... -
Find_primer_sequence_and_reverse_complement_read_within_amplicon.fastq script needed
Hi,
I have a fastq file with merged amplicon sequence reads post Illumina sequencing. However, the library was build by ligating the Illumina... -
Find out if you have amplicon reads.
Is there really no way (program, tool) to tell if your BAM files have amplicon reads?
How is everyone doing it? determining a priori and... -
MiSeq Sequencing Short Amplicons
Hello,
If I am sequencing a heterogeneous mixture of amplicons using a MiSeq (2x250bp) to ensure overlap, and there are some short amplicons... -
Multiplex PCR missing some loci/low template
I am trying to multiplex 12 primer sets in a single PCR. The goal is to amplify 12 taxon-specific loci from environmental samples. So, 1) DNA concentrations... -
Variable per tile sequence quality across amplicon-seq fastqs
I sequenced numerous amplicon-seq libraries today and found the sequence per tile quality to be highly variable across the fastq files. I initially thought... -
Failed index reads with homegrown adapters
Hi,
I'm hoping someone can help. I am trying to sequence amplicons on the MiSeq with adapters and barcodes we have designed in the lab.... -
incredible high memory consumption of bwa-mem on small amplicon dataset
Hi all, I am working with Human amplicon data and have been using bwa mem (0.7.15) up to now. Unfortunately, on some datasets the memory consumption exceeds... -
NextSeq having problem sequencing amplicons with stretch of C
We seems to have problem sequencing several different amplicons with a stretch of C on the NextSeq using v2 chemistry 300-cycle kits. This happen to 2... -
Amplicon consensus calling from sub-reads
Hi everyone,
I just got my first PacBio data in and would like some advice on how to handle the data. I submitted a 1KB amplicon library...
