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Hi, @etal !
When I run CNVkit pipeline (v0.9.7) in wgs mode to make tumor analysis,
command: `$CNVKIT batch /data/D2288/D2288_t.aligned.bam --normal /data/D2288/D2288_n.aligned.bam --seq-method wg…
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cutadapt 4.4
python 3.10
pip 22.0.2
I am using Cutadapt to demultiplex my amplicon sequencing data, and I am reporting the number of amplicons detected under adapters_read1 in the JSON report, af…
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Dear Bjorn,
Thanks for the program! It is the perfect solution for my search of establishing my lab under Open Science principles. Yesterday we tried pydna for the first time and we encountered a sm…
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Dear Prof
I trust you are keeping well
I want to know, that is it necessary to have phylogenetic tree for this model, or we can use this with out tree
kindly please let me know
Thanks and Regards
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Hi there,
Thanks for this great container, very helpful.
However, I have some troubles at species and pathovars level.
1) I need primers for a particular bacterial species. There are 14 genomes a…
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ghost updated
3 years ago
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Hello, During the rule_reformat_filter_clusters step, only 36% of the clusters are being written, and I am not sure why. I understand this is happening in parse_clusters.py but have not been able to i…
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I am experiencing issues with the sequence alignment of my FASTQ file with my amplicon sequence as I receive the following error message "It was not possible to align any read to the reference amplico…
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[combined_seq_412.fastq.gz](https://github.com/USDA-ARS-GBRU/itsxpress/files/5048580/combined_seq_412.fastq.gz)
`/home/ubuntu/miniconda3/bin/itsxpress --fastq /home/ubuntu/combined_seq_412.fastq.gz -…