From Array Suite Wiki

Bacterial counts from 16S rRNA

LandView 16SMicrobial NR 025588.1.png


As part of the Land RNA-seq pipeline, OmicSoft has quantified the number of reads mapping to bacterial 16S rRNA in each sample. These data can be visualized in several Lands with the 16S Microbial View.

LandView 16SMicrobial Menu.png

16S microbial data are from NCBI reference sequence. We align unmapped reads from RNA-Seq bam files to these bacterial 16S Ribosome RNA gene sequences, and counted the total reads for each bacterial 16S sequence. Next we normalized the read counts by the total mapped reads of a sample.

Land Data Requirements

The 16s Microbial Variable View is available for several Lands in OncoLand, including TCGA, CCLE, and GTEx. Only samples with RNA-seq data will be included.

Features of the 16S Microbial Variable View

For each microbial 16S rRNA sequence, one plot will be generated. In each plot, samples will be grouped by the specified grouping, such as Tumor Type, and the number of RNA-seq reads matching the 16S rRNA will be plotted.

Tips.pngBacterial 16S rRNA reads are normalized in each sample by 1,000,000 * (16s read count) / (reads mapping to human genome).

Samples will be colored by secondary grouping, such as Sample Type.

In addition to filtering by sample metadata, the user may filter the displayed microbial species under the 16SMicrobial filter tab:

LandView 16SMicrobial FilterTab.png

The user can also view a list of the microbial sequences passing the filter settings by clicking View Filtered Table:

LandView 16SMicrobial ViewFilteredTable.png

LandView 16SMicrobial ViewFilteredTable Table.png

Related Articles