Extended Data Fig. 1: Additional comparison of RNase I RPF libraries by ligation-based or OTTR protocol.

a, Fraction of RNase I RPF sequencing library reads that mapped to each transcript class. Library generation artifacts included sequences that were adapter-only, shorter than 15 bases, or unmapped. b, CDS RPF length distribution from OTTR (blue) and ligation-based (red) RNase I ribosome profiling libraries. RPFs aligned to the first 15 or final 10 codons were excluded. Counts were represented in reads per million mapped reads (RPM) and averaged across replicates. c, For each read length from 26 to 29 nt, the fraction of RPF alignments with mismatches at the 5′-most base of the alignment. For this analysis, alignments were permitted to only have a single mismatch to the reference. d, For each read length from 26 to 29 nt, the fraction of RPF alignments with an adenosine (A) at the 3′-most base of the alignment. For this analysis, alignments were permitted to only have a single mismatch to the reference. e, For each read length from 26 to 29 nt, the fraction of RPF alignments with a thymine (T) at the 3′-most base of the alignment. For this analysis, alignments were permitted to only have a single mismatch to the reference.