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I have 200 metagenomes extracted from stream biofilms. I binned contigs to obtain MAGs and I dereplicated MAGs obtained in all samples to obtain a final pool of MAGs. Finally I mapped reads from each …
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Hi there, when i use SMTa for microbe analysis in visium data and run SMTa start from spaceranger output
(Human Intestine Cancer (FPPE) data from https://www.10xgenomics.com/datasets/human-intestine-…
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Hi @benjjneb
I have a new batch of sequenced samples that have been 16S sequenced using PacBio technology. I have two significant issues when processing the reads using DADA2 pipeline for PacBio:
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I am trying to run Canu to assemble some nanopore reads. I have attempted some fixes from other threads but I am a little stumped on how to resolve this. Does anyone have any suggestions?
Command:
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I am currently running through the tutorial for dada2, test running everything as I go, got cutadapt installed, and then did a test run of it to get the version #.
> cutadapt system2(cutadapt, ar…
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I found issue #521 but none of the tips there helped in my case.
I am trying to run bactopia on WSL + Ubuntu, fresh install. Installed MambaForge as per the installation instructions, then installed …
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Simple premise: use merge_samples to do exactly that but on different "merging" functions. Specifically: mean (the default), sd, and sum. In R terms:
md1 = merge_samples(OTU,"descriptor",fun=mean)
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Hi,
I am using sortmerna to calculate coverage and abundance of reads from rRNA predictions (using MATAM) on the metagenomic libraries. However, the folders out and readb are always empty. Any reaso…
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Beginning with sequence-based searches of the literature via PaperBLAST and using the sequences acquired from PomBase, UniProtKB
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Hi all,
First, thank you for all the work that you do on maintaining this package, it is truly invaluable for microbiome analysis.
I'm trying to process ~1100 dental plaque samples. These are V…