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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,
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,
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,
The query reads is GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG. Its alignment informatio…
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I couldn't find this documented anywhere, and looking through the code, I couldn't figure it out myself. I see a `num_qstrat` parameter in [medaka/features.py](https://github.com/nanoporetech/medaka/b…
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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 …
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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! 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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Helllo
My name is Andrea, and I am currently working with a set of SARS-CoV-2 sequences obtained by Illumina tech in order to find different SNVs that lead to the identification of viral quasispec…