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Before doing runs, I have been filtering out samples in the Viridian dataset based on two criteria: (1) having full-precision collection dates, and (2) having at most 800 Ns (excluding gaps) in the _*…
szhan updated
4 months ago
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Can we use Snippy for phylogenetic tree construction for COVID-19 from Fastq reads. If not, Can you suggest some tool to work with fastq reads
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The accession BK010471 is for a crAssphage that is ubiquitous in human gut metagenomes ([link](https://www.nature.com/articles/ncomms5498)), and in particular is found in the 454 data set SRR073439.
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Hi,
I am quite new in the BCR/TCRsequencing field and I wanted to try to compare TRUST4 and MIXCR on a simple dataset (amplicons of the CDR3 regions).
I have a paired end fastq with about 20'000 r…
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Hello!
I am processing ITS data with DADA2 (primers ITS1F-ITS2). I am following recommendations from this paper (https://www.sciencedirect.com/science/article/pii/S1754504818302800?via%3Dihub) and fo…
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Hello,I meet a question about prepare the bed file for AA.
my command:
python /home/tang/tools/PrepareAA/PrepareAA.py -s A549 -t 4 --cnvkit_dir /home/tang/tools/cnvkit/cnvkit.py --sorted_bam /home…
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```
hp_pairwise_align --amplicons_fa haphpipe_assemble_02/final.fna --ref_fa ../HIV_B.K03455.HXB2.fasta --ref_gtf ../HIV_B.K03455.HXB2.gtf --outdir haphpipe_assemble_02
[--- pairwise_align ---] U…
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In a test run with [`mdasim 2.1.1`](https://github.com/hzi-bifo/mdasim/releases/tag/v2.1.1) on the example input data and using the testing pipeline, I got the following `example_input.example_mdasim_…
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Hello,
i saw you're already have a pipeline for preprocessing single-cell DNA-seq. I was wondering if it would work for tapestri data ?
Thanks you in advanced for your answer.