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Hello,
Thanks to develop this fantastic pipeline.
I'm looking forward to reading your paper!
I have amplicons from a nanopore metabarcoding run that did not span 16S rRNA gene but another gene.
I…
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Hi @mikemc
Thanks for your email.
I am new to R and Phyloseq. However, I need to analyze the 16S rRNA data (please see the attached file for data format). I have the otu-tables & absolute abund…
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### Description of feature
sortmerna is implemented in the pipeline and runs by default. There will also be a bunch of other short RNA species we should remove, which we can use the (also inherited) …
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Dear Alex;
I am performing RNA sequence analysis to determine the DE genes in a human cell line sequenced with Ion Proton. I am using the default STAR settings and I get a low percentage of uniquel…
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Dear Developer,
Hello! Thank you very much for developing such a convenient software for our use. When we were running the RepeatExplorer software on Galaxy, we intended to obtain the consensus seq…
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I see that this package uses the GreenGenes database of 16S rRNA genes. Depending on which version you're using, this database is potentially outdated. Could you let me know which version of GreenGene…
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Hi Donovan,
Am having an issue with the ssu_erroneous command. The output is given below. What seems o be the issue here?
$ refinem ssu_erroneous -x fasta metagenome_test/ taxon_profile_output/ gt…
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Hi,
I have paired-end (2X100) RNA-seq data of variable post-trimmed length (2X36-100nt). For a good fraction of samples, I am getting very low uniquely mapped reads % and very high% of reads to mult…
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Not sure how we can add this functionality, but it would be more correct to calculate UniFrac using a tree with branch lengths determined by e.g., a 16S rRNA gene multiple alignment and evolutionary m…
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Hello,
I'm running STAR (STAR-2.7.9a) inside of a snakemake pipeline and it uses this command:
$STAR --genomeDir outputs/star_index --runThreadN 5 --readFilesIn outputs/reads/rrna_filtered/s1.1.fq…