Questions tagged [metagenome]

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Kraken2 > OTU format > Phyloseq

A collaborator has passed me over Kraken2 outputs *.report and *.kraken, from a metatranscriptomic sequencing experiment conducted on the minION. I would like to make a tree if the data using a ...
Reebola95's user avatar
2 votes
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MAGs transcriptomics pipeline question

I have currently a following problem. I have a one sample that I did my metagenomics on (Illumina shotgun + nanopore) and have recovered some high quality MAGs. I also did a metatranscriptomics on the ...
Avamys's user avatar
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Krakenuniq mmap error

I built Krakenuniq on an HPC, and I've been trying to run it on my data using the following command: krakenuniq --db DBDIR --threads 1 All_reads.fastq This ...
schmiggle's user avatar
2 votes
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Does it make sense to compare the mean relative coverages for contigs / MAGs from samples that were not co-assembled?

I have a subset of high-quality MAGs from different environments, sequenced on different runs. I want to know, for any particular MAG, if it (or something similar to it) is present in any particular ...
Laura's user avatar
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How to apply RDP, Greengenes and other special taxonomies in Krona?

I used Kraken 2 to classify my 16S metagenomic data using both RDP and Greengenes database. As these are special databases the taxonomic ids assigned do not match with the NCBI taxonomic ids. I found ...
Ahmed Abdullah's user avatar
1 vote
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Can files with different R1 and R2 lengths be trusted?

I received paired end amplicon sequence from a LAB with different lengths for R1 (320) and R2(280). Should I trust this lab to sequence other samples? Also, I had to do a trimming over the R2 at 220(...
abi's user avatar
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Bracken not working

I have some highly contaminated ancient DNA sequences. I have adapter removed and collapsed these and run them through Kraken2. The Kraken reports show multiple levels of taxa with good numbers of ...
Andy Walton's user avatar
1 vote
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Transcriptome analysis

I am trying to assemble reads belonging to two different readlength. Is it a valid way since I am looking for common genes among the species I am assembling.
julierebecca's user avatar
1 vote
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Removing adapters + primers from fastq files

I am currently in the process of removing adapters and primers from some 16S data acquired, and have a conceptual question regarding this pre-processing step: So there are a series of different primer ...
h3ab74's user avatar
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1 vote
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Which database is good to store (metagenomic) relative abundance data?

The simple question is: how to store relative abundance data in a database? Which database to choose? I am talking here about metagenomics data, relative abundance of species or some features. Each ...
Art's user avatar
  • 111
1 vote
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Analyzing and visualizing metagenomic data

I am starting out in metagenomics, Aim I wish to understand the whole analysis from the raw reads to interpretation. Background My current pipeline is used for: analyzing human gut microbiota cleans ...
Roger V.'s user avatar
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Alternatives to phrap for merging contigs with overlapping ends?

I have bins from metagenomes generated with metabat2 on bitbucket/berkleylab/scr which are predicted as viral by MARVEL. MARVEL ...
Stanley Ho's user avatar
-1 votes
1 answer
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Feature-selection microbiome data to build a model to predict cancer

I want to build a machine learning model to predict colorectal cancer based on 16S rRNA microbiome data (stool samples). I have filtered the data using filtering approach by Duvallet(removing samples ...
user17818805's user avatar