User: richard

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richard0
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Posts by richard

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Answer: A: Paired-end metagenomics data for MEGAN analysis
... http://megan.informatik.uni-tuebingen.de/t/paired-end-read-analysis-diamond-megan/1340 Try this ...
written 3 months ago by richard0
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Comment: C: Centrifuge - Error: reads file does not look like a FASTQ file
... Figured it out, Something was corrupted in my reverse reads, going to re-download them. Thanks again! ...
written 3 months ago by richard0
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Comment: C: Centrifuge - Error: reads file does not look like a FASTQ file
... Thanks, will do and will get back to you ...
written 3 months ago by richard0
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Comment: C: Centrifuge - Error: reads file does not look like a FASTQ file
... sure, but thats not the issue. It is in ` ` parentheses in the actual code, which I couldn't post here. The issue is that centrifuge is throwing an error about my fastq files ...
written 3 months ago by richard0
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Centrifuge - Error: reads file does not look like a FASTQ file
... I am getting the error that my fastq files are not actual fastq files from Centrifuge. Not sure what is wrong with my files. They seem like normal fastq files and have run successfully through other metagenomic pipelines like metaphlan2, but fail with Centrifuge. Here is prep & my command: ...
centrifuge metagenomics fastq shotgun written 3 months ago by richard0 • updated 3 months ago by h.mon29k
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Comment: C: Reference genome for microbiome WGS metagenomics ?
... Ideally in-depth analysis but for many samples. At first I want to do taxonomy, but later may look into gene pathways present. ...
written 3 months ago by richard0
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Comment: C: Reference genome for microbiome WGS metagenomics ?
... The goal is to do WGS Shotgun sequence taxonomic profiling from human stool samples. Im trying to understand the benefits of interrogating a larger database like NCBI or Ensembl versus using the smaller curated database of Metaphlan2. ...
written 3 months ago by richard0
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Comment: C: Reference genome for microbiome WGS metagenomics ?
... Thank you, will check it out ...
written 3 months ago by richard0
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Comment: C: Reference genome for microbiome WGS metagenomics ?
... The goal is to do WGS Shotgun sequence taxonomic profiling from human stool samples. Im trying to understand the benefits of interrogating a larger database like NCBI or Ensembl versus using the smaller curated database of Metaphlan2. ...
written 3 months ago by richard0
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Reference genome for microbiome WGS metagenomics ?
... Which reference database is really the best ? I know metaphlan's data base has 17,000 species and 1M marker genes, but the Ensembl database has 40,000 bacterial genomes. Any ideas on what is best ? ...
microbiome metagenome metaphlan2 ensembl written 3 months ago by richard0 • updated 3 months ago by mschmid150

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