Table 2. Summary of data analysis with supplementary scripts A-G (located at the repository: https://github.com/gfkramer/SeRP_yeast).

No	Name	Description	Input	Output
A	Ribosome_Assignment	General data analysis comprises the assignment of the ribosomal A-site for each footprint.	SAM file from genome alignment, A-site offset (txt file) in case of ‘5-end’ mode	no.of reads at each position along the genome (pkl file) distribution of footprint lengths (txt file) gene expression (txt file)
B	3_nt_Periodicity	The average ribosome density of all included transcripts is visualized to check the periodicity. Similar to a metagene profile but on nt scale.	no.of reads at each position along the genome (pkl file) from A	metagene profile with nt resolution (figure)
C	Footprint_Length_Distribution	The calculated footprint length distribution is visualized as dot plot.	distribution of footprint lengths (txt file) from A	distribution of footprint lengths (figure)
D	Tota l_Enrichment	The expression of each gene is compared between selective and total data sets, 2 biological replicates required.	gene expression (txt file) from A	total enrichment for each transcript (txt file)
E	Transcript_Profiles	An enrichment profile is plotted for each transcript.	no. of reads at each position along the genome (pkl file) from A	transcript profiles (figure)
F	Binding_Detection	The enrichment of selective over total translatome is statistically analyzed to identify factor- binding regions.	no. of reads at each position along the genome (pkl file) from A	number, localization and length of each binding region (txt file)
G	Metagene_Profiles	The average profile of all included transcripts is plotted for the selective and total data set and the enrichment of both.	no. of reads at each position along the genome (pkl file) from A	metagene profiles (figure)