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I'm a new dada2 user and I've been struggling with 2 datasets 2x300 amplified using primers 27F and 519R. The samples are from microbiome of algal cultures.
The reverse reads are quite bad quality, b…
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Hi, I did indexing for bovine genome reference UMD3.1, and am doing the further alignment.I have encountered Chromosomal sequence could not be extracted errors when processing trimmed WGBS FastQC data…
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Hi there,
We've been analyzing a batch of 18S mock communities using DADA2. We put the mock communities together by mixing 22 unique, cloned, full-length 18S amplicons (Sanger sequenced before mix…
dcat4 updated
5 years ago
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Hello Pierre,
I have a conceptual problem. For a set of query sequences coming from metagenomic origin, I want to know the taxonomy. I have a reference tree with ~600 sequences. Should I:
- Pe…
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A small subset of sequences in CAR (and other AMR databases) have not been reverse-complemented in their FASTA representation. This is inconsistent with the other entries.
Some entries do revcom t…
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I am new to nanopolish and here is a question I can't find an answer.
After running "nanopolish variants --consensus", I ended up with an unchanged consensus sequence and this summary: [post-run sum…
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Hi!
I am currently trying to run the following command:
`racon -u -f -w 50 -q 9 ../trim50_dem_q9/barcode02.fastq ../minimap2_output_x_map_ont/aln_2.sam ../gene_references/msp2_pf3d7_02026800.fasta`
…
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I'm using cutadapt 2.4 and Python 3.6.8 installed with pip3.
When demultiplexing using linked adapters and pair-end reads I recognize that cutadapt does favor a shorter partial overlap that would i…
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Dear Luca,
I have been trying to figure out how to incorporate the QC parameters for trimmomatic (LEADING TRAILING SLIDING WINDOW MINLEN) into the CRISPResso command. I can run the following comman…
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For example, polyN have trouble to sanger sequencing, therefore it is better not to place primer pairs around it.
The tag `SEQUENCE_EXCLUDED_REGION` is not suitable, as it tells primer3 to exclude …