Workflow differences between hg19 and hg38

[kodalivk]

Hello,
I have a question about the procedures followed for mapping data to hg19 and hg38. Was the workflow same for both? If I understand correctly, the method described in Michel et al., 2014 was used for hg19 data. When new data were mapped to hg38, was the same workflow employed, including the use of RUM to map intron-spanning reads? The workflow published in RiboGalaxy (https://ribogalaxy.ucc.ie/u/vimalkumarve...-may-2015) does not have the RUM step. Was this done outside Galaxy?

For example, if we look at the example of a gene RPS23, hg19 data clearly supports translation initiation in exon 1 which encodes only the methionine (https://goo.gl/iDCo5h). However, looking at the hg38 data (https://goo.gl/v8a672), the initiating ribosomes' profile nearly mirrors that of the elongating ribosomes' profile. I imagine this would occur if some reads aligning to exons 1 and 2 were dropped when mapping to hg38 and such reads would be enriched in the samples treated with a drug to arrest ribosomes in the initiator site.