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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 Depending on which version you're using, this database is potentially outdated.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,
Apologies if this is in the documentation somewhere.
Is there an option in Stringtie to use a mask file (to ignore rRNA, pseudogenes etc?)
Many thanks.
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This would likely make a good worked example / test case:
> Landa et al. (2021) Diversity of Phytophthora Species Detected in Disturbed and Undisturbed British Soils Using High-Throughput Sequencin…
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Hi,
I am using star-align and star-fusion to detect fusions with RNAseq data. I initially aligned fastq files to the rRNA reference genome to remove rRNA reads. Then I collected the unmapped reads …
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Torsten-
An idea for enhancement: would be great to have an option for barrnap to write fasta file(s) containing just the detected rRNA sequences, i.e. to slice the input contigs file at coordinates r…
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Hi,
I'm using `bam_vs_bed` to quantify the number of reads that are aligned to different transcript types (RNASeq) using a bed file where the ID is a gencode gene_type. The output for one sample is…
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Right now, release binaries *.tar.gz files only contain the `sortmerna` binary file.
At a minimum, we should include a README file, the LICENCE file, and either the rRNA databases or a script to down…
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#### Is your feature request related to a problem? Please specify.
I've encountered a few cases where markdup has crashed due to using extreme amounts of memory (>100GB). I'm unfortunately not able t…
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Hi, I am trying to build my own Sourmash LCA database based on NCBI, SILVA, or Greengenes databases for taxonomic classification for my k-mer hash dataset (e.g. 7-mer) computed from 16S rRNA gene sequ…
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Discusses qPCR, RNA sequencing, single-cell RNA sequencing, and 16s rRNA Gene (DNA) sequencing.
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