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coverage profile - singhk2@mskcc.org - 05-May-2015 06:12 PM

Hi
How are the peaks for the coverage profiles are generated.
Thanks
Kamini


RE: coverage profile - audrey - 06-May-2015 08:56 AM

Hello Kamini,

The coverage files display the number of sequence reads that align to each coordinate. In other words, the number of sequence reads that "cover" a particular genomic coordinate are counted and displayed as a bar.

Ribosome profiles, for the eukaryotic datasets, display the coordinates of the A-site (for elongating ribosomes) or the P-site (for initiating ribosomes) that are inferred from each sequence read by adding a specific offset to the coordinate of the most 5' nucleotide of the read.

For the prokaryotic datasets, a center-weighted approach (Oh, E. et al. Cell 2011, 147, 1295–1308) is used to indicate the most likely positions of the ribosome A-site.

Hope this answers your query and if not please let us know.