Computational protocol: Genome Wide and Experimental Resolution of Relative Translation Elongation Speed at Individual Gene Level in Human Cells

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Protocol publication

[…] For ribosome profiling datasets, the adapter sequences were removed from all reads. Reads were truncated at their first nucleotides, whose Phred quality scores were less than 10. Reads shorter than 18 nt were then discarded. The rest high quality reads were aligned to the RefSeq-RNA reference sequence (downloaded from http://hgdownload.cse.ucsc.edu/downloads, accessed on Jan. 21st, 2013) using FANSe 2 algorithm [] with the parameters –L60 –E2 –U1 –S10. For mRNA and RNC-mRNA sequencing datasets, the reads were mapped to RefSeq-RNA reference sequence with FANSe2 algorithm with the parameters #x2013;L55 –E4 –U0 –S10. Alternative splice variants were merged []. The expression levels were estimated by using the rpkM unit []. The mRNA length information was also acquired from RefSeq. […]

Pipeline specifications

Software tools FANSe, FANSe2
Organisms Homo sapiens
Diseases Neoplasms