User: shengwei

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shengwei30
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Posts by shengwei

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Answer: A: trinity metatranscriptome assembly without reference genome
... I think it also depends on your objectives. Metagenome assemblies are great as DNA references, but if you're also interested in the RNA viruses, you can't rely on metagenome assemblies. And some low abundance organisms might be very actively transcribing, then you won't get them if your metagenomic ...
written 4 months ago by shengwei30
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Answer: A: Normalization methods for metagenomics WGS data (not 16S data)
... You can try [ALDEx2][1] as well, it deals with compositional data using log-ratio transformation. [1]: https://bioconductor.org/packages/release/bioc/html/ALDEx2.html ...
written 6 months ago by shengwei30
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Comment: C: Cazy Database Sequences Download
... There is an updated version here: http://bcb.unl.edu/dbCAN2/ ...
written 8 months ago by shengwei30
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Comment: C: output TMM normalized counts with edgeR
... This is not accurate, the default returned value is not log2 transformed according to the documentation: ## S3 method for class 'DGEList' cpm(y, normalized.lib.sizes = TRUE, log = FALSE, prior.count = 2, ...) ## Default S3 method: cpm(y, lib.size = NULL, log = ...
written 8 months ago by shengwei30
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Answer: A: Download SAM/BAM files from SRA takes ages!!!
... check [here][1] for an example using Aspera Connect (ascp): 1. To download prefetch --max-size 100G --transport ascp --ascp-path "/path/to/aspera/3.6.2/bin/ascp|/path/to/aspera/3.6.2/etc/asperaweb_id_dsa.openssh" --output-file $OUTPUT_DIR/$SRA_ID.sra $SRA_ID 2. To extract fastq-dump - ...
written 20 months ago by shengwei30
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Answer: A: Cazy Database Sequences Download
... I use [dbCAN][1], it's based on CAZy database and regularly updated. You can annotate your protein online, or download the database then do blastp/hmmscan search locally. [1]: http://cys.bios.niu.edu/dbCAN2/ ...
written 3.9 years ago by shengwei30

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Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: Cazy Database Sequences Download

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