# List the ribosome profiling bam/sam files below and specify the lengths and P-site locations of alignment reads which
# are most likely originated from the translating ribosomes. If multiple files are defined, their P-site densities along
# each nucleotide would be added together.


# Explanation of each column:
# 1. SampleName: specify a name for each sample
# 2. AlignmentFile: ribosome profiling alignment file (bam or sam format) at the transcript-level
# 3. Stranded: Strandedness. Specify 'yes' for stranded interpretation, 'reverse' for reversed strand interpretation, or
#              "no" for non strand-specific libraries.
# 4,5. P-siteReadLength, and P-siteOffsets: the read lengths and P-sites locations.
#      Both of them can be estimated by perform the metagene analysis using our package.
#      List all lengths or P-site locations which separated by ",".

# SampleName	AlignmentFile	Stranded(yes/reverse) P-siteReadLength P-siteLocations
HEK293_ribo HEK293Aligned.toTranscriptome.out.bam yes 26,27,28,29 12,12,12,12
