Hi,
I am new to ribosome profiling but am hoping I can use the RiboProfiling package for analyzing my data. I want to customize where I am looking for protected fragments though because I would like to not include the start region (the first 50 nucleotides) for all transcripts as it can sometimes result in a biased comparison between genes. Is there a way I can use this package and specify that I would like to not count reads that fall on the first 50 nucleotides of every transcript? I tried using the listshiftvalue parameter but the output I got in the data.frame is the same as when I didn't add 50 there so I think this must be the wrong place. 
covData <- riboSeqFromBAM(listInputBam, txdb = txdb, listShiftValue=c(50))

Thank you! 

Angela Nicholson