ARW-UBT
ARW-UBT
Hello, I found a few contradicting posts in bioinformatics forums whether Megahit could be used or must not be used for metatranscriptome assemblies from microbiome meta-RNA-seq data. I have it...
Hi David, we have installed degust in docker and it is a great tool! Thanks for that. I would appreciate if you could answer a few specific questions: 1) Is...
Hello, I have selected a tab-delimited count table and a tab-delimited metadata file for upload to your web instance of DEBrowser. The status bar below each selected files states 'upload...
Hi, is there a possibilty to test whether a mysql configuration is properly set up on linux for PASA? The 'test' command does not allow specifying '--pasa_db mysql'. Best regards
Hello, I am using a reference genome of Folsomia candida available via NCBI's datasets for RNA-Seq expression studies. A part of the gene/transcript annotation contains multiple mRNA / CDS annotations...
Hi, I read about StringTie and I am wondering whether it could be used to de-novo assemble a transcriptome from RNA-Seq data using a genome of a closely related species...
Hi, I have analysed ITS1 amplicons from fungal samples (leaf endophytes) using kraken2 and the PlusPFP-16 indices provided by Ben Langmead. These amplicons were trimmed for PCR primer sequences, but...
Hello, we have analyzed 16S amplicon data with Kraken2 and subsequent Bracken quantification, Both report files could be imported to Pavian, but the Bracken report files do not display any...
Hello, I was using empress as a visualizer for phylogenetic trees produced in qiime2 releases up to v. 2024.2. It seems that empress is to some extent incompatible to q2-2024.5...
Hello, I am using dada2 as implemented in Qiime2 on single-end ITS amplicons with great success! Thanks for dada2! For a more detailed investigation of fungal diversity in environmental samples,...