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Hi Ben,
I have been using DADA2 on illumina sequenced COI data for the last year and it has become the backbone of my bioinformatics pipeline. We now have a PhD student in our group developing meta…
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Hi,
I am using Clair3 for variant calling on targeted amplicon sequencing data. Since we are using the R10 flowcell and the model provided by ONT was trained at 60x depth, we subsample the bam to 60x…
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It seems like ARTICv4.1 Amplicon 74_LEFT primer has a mismatch relative to currently circulating XBB lineages. As a result, assemblies for these lineages will have a dropout in the Spike gene (positi…
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Hi,
The query reads is GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG. Its alignment informatio…
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Hello,
I am utilizing a scTCR protocol where it uses dual indexing to barcode each cells. Basically, the protocol states,
"the amplification reaction contains flanking rhPCR primers ([Suppleme…
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Hi! Thank you for the tool! I tried to deduplicate my Bismark alignment in WGBS data and I found that the duplication rate is very high (70-80% duplication).
Here is a example deduplication_report.…
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Hi, I tried to run the command as below, but the alignment is 0, I don't know why, could you please help me to find out the reason?
module load crispresso2
CRISPResso -r1 gAE1-H_R1_001.fastq.gz …
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Hi @benjjneb ,
I'm inquiring into the maximum sequence length allowed for DADA2 1.12.1 analysis. According to your 2019 PacBio paper, the maximum sequence length allowed is 3000 nucleotides. In the…
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Hi,
First of all thank you for providing us this tool, it may help a lot,
We are working on amplicon-based long read sequencing ONT and I want to tag reads in BAM file according to their respectiv…
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Hello Jared,
I had ~20000 amplicons from one locus sequenced by a R10 flow cell from Oxford Nanoporetech, then mapped the reads by graphmap, converted to bam, sorted and indexed with samtools and …