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(crispresso2_env) YudeMacBook-Pro:NGS shwan$ CRISPRessoPooled -r1 PE-reporter-seq-LGC16574_L2_1.fq.gz -r2 PE-reporter-seq-LGC16574_L2_2.fq.gz -f AMPLICONS_FILE_PE_reporter.txt --name ONLY_AMPLICONS_24…
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I'm trying to run DADA2 via QIIME2 and noticing that it's very hands-on and not completely automated.
**Are there any reliable tools that can indicate where I should trim my forward and reverse rea…
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Hello @benjjneb,
Thanks for dada2 we are following your ITS pipeline, but are having issues with some unexpected read loss. We find ourselves losing a large majority of our fungal reads and we are …
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Hi Dr.Chen,
I’m writing this issue because I want to clear up some confusion about the exact working of paraphase.
Firstly, I’m using amplified PacBio Hifi data to analyse the PMS2 region. E…
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### Is your feature related to a problem?
Most people doing environmental samples do amplicon sequencing for mixed communities so it would be convenient to have a solution for handling this kind of d…
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Dear dada2 enthusiasts,
Upon analyzing my HTS (Illumina Miseq 2x300bp) data generated after amplification of the CO1 I3-M11 fragment (ca. 396 bp without primers) I am faced with doubts about the co…
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The paper that describes the method mentions single-cell transcriptomics, CyTOF, and microbiome sequencing as applications. I have read the paper and description of the statistical model and I am appl…
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These SNPs look true on IGV. Why are they labelled as RefCall by Clair3? The AF values in the output VCF are around 0.5.
Another question: Clair3 is to find germline variants. However, my data is…
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Hello again,
I wanted to ask a clarifying question about trimming multiple adapters from paired end reads. I detected Nextera and small RNA 3' adapter. I then trimmed these by running trimgalore tw…
mjbug updated
3 months ago
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Hi,
I would like to use UMI-tools to compute a consensus sequence from a 'read group'. Is this modification possible?
Thanks!