HEK: Calviello 2016 Track Settings
 
Detecting actively translated open reading frames in ribosome profiling data. (Calviello et al. 2016)   (All Elongating Ribosomes (A-site) tracks)

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     ribosome profiling  Ribosome Profiles of elongating ribosomes from Homo sapiens (Calviello et al. 2016)   Schema 

Description

Examination of RNA fragments protected by ribosome

Methods

Raw sequence data were obtained from NCBI FTP directory(SRP063852). Data from the following samples were processed:

ribosome_profiling Ribosome profiling data from Homo sapiens(Calviello, et al. 2016)

Adapter sequences had already been removed from reads. An alignment to ribosomal RNA was performed using Bowtie, and aligning reads were discarded. An alignment to the hg38 genome assembly was performed using Bowtie, and reads below 25nt were discarded. These tracks contains the uniquely mapping reads.An offset of 15 nucleotides was then used to get the corresponding A-site of each read.

References

Calviello L, Mukherjee N, Wyler E, Zauber H, Hirsekorn A, Selbach M, Landthaler M, Obermayer B, Ohler U (2016) Detecting actively translated open reading frames in ribosome profiling data. . Nat Methods. 2016 Feb;13(2):165-70. doi: 10.1038/nmeth.3688. Epub 2015 Dec 14. Research Support, N.I.H., Extramural