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Metagenomic Analyses

Nucleotide periodicity of mapped reads

All mapped reads are aligned by their 5' ends. Ribosome-footprint reads exhibit a three-nucleotide periodicity along the ORF. Footprinting reads also show accumulation at the start and stop codons.

Read count histogram

Distribution of lengths of reads mapped to coding sequences.

Position-specific distribution of reads

Metagene analyses of RPF and RNA-seq reads. Mapped reads at each position (codon for RPF and nucleotide for mRNA) are normalized by the mean within each ORF, and then averaged with equal weight for each position across all ORFs. The size of the RPF 'ramp' varies between studies and can be largely attributed to use of CHX pre-treatment. Each RPF dataset is compared with an average of representative studies with and without CHX pre-treatment. Each mRNA dataset is compared with an average of representative studies. Shaded areas represent standard errors around the mean lines.

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Excess codon-specific RPF reads in 5' ends of ORFs

For each of the codons, densities of RPFs with ribosomal A sites mapping to that codon were calculated using either only the ramp region of each ORF (codons 1-200) or the remainder of each ORF. Datasets with CHX pre-treatment typically have higher excess codon-specific reads compared to non-CHX datasets. Shaded areas represent standard deviation.

Nucleotide frequencies along mapped reads

All mapped reads of a particular length are aligned and nucleotide frequencies are estimated at each position.

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tRNA abundances and codon-specific reads

Correlation between codon-specific normalized reads mapped to either A, P, or E-site of the read and various estimates of tRNA abundances.

Sequence-based features and normalized reads

Correlations between coding sequence features and gene-specific RPKM values. Correlations are estimated based on genes with at least 64 mapped reads (blue dots).

Gene based analyses

Gene by gene analyses are available here or through the Gene of interest tab.

© 2017 Oana Carja and Premal Shah