A FASTQ file is a special type of text file that contains the sequencing data. Each read has four lines:

•  Line 1: sequence identifier
•  Line 2: the reported base calls
•  Line 3: a separator
•  Line 4: the quality scores

A BAM file is a compressed binary file that contains a header (summarizing the entire file) and the aligned reads (read name, position, and alignment quality).

The index file is required for visualization in a genome viewer such as IGV.

A bedGraph file is used to display continuous data in a genome browser. These bedGraph files show coverage of 5' ends of reads at each position. Files ending in .snt_pos.bedgraph are only the reads mapped to the “+” strand, while files ending in .snt_neg.bedgraph are only the reads mapped to the “–“ strand.

A BED is a tab-delimited file that can be used to visualize data on a genome browser. The ends.bed file represents locations of single nucleotide resolution end calls identified using the PureCLIP algorithm. It has the following columns:

•  Column 1: chromosome
•  Column 2: start position
•  Column 3: end position
•  Column 4: state. The state is always "3", which corresponds to the enriched and crosslinked state within the PureCLIP tool.
•  Column 5: score. The score is the log posterior probability ratio of the first and second most likely states identified by the PureCLIP algorithm
•  Column 6: strand (+ or -)

A BED is a tab-delimited file that can be used to visualize data on a genome browser. The ends.best.bed file represents locations of single nucleotide resolution end calls identified using the PureCLIP algorithm, and filtered of false positives derived from dT mispriming. It has the following columns:

•  Column 1: chromosome
•  Column 2: start position
•  Column 3: end position
•  Column 4: end ID
•  Column 5: score. The score is the log posterior probability ratio of the first and second most likely states identified by the PureCLIP algorithm
•  Column 6: strand (+ or -)

This file is only included if the experiment contained replicate samples. A BED is a tab-delimited file that can be used to visualize data on a genome browser. The reproducible_ends.bed file represents locations of filtered ends found to be reproducible across all replicates of a condition. It has the following columns:

•  Column 1: chromosome
•  Column 2: start position
•  Column 3: end position
•  Column 4: geometric mean score. The score is the log posterior probability ratio of the first and second most likely states identified by the PureCLIP algorithm
•  Column 5: unused column (.)
•  Column 6: strand (+ or -)

The table summarizes differential end usage analysis between two sample conditions. It has the following columns:

•  Column 1: chromosome
•  Column 2: start position
•  Column 3: stop position
•  Column 4: strand
•  Column 5: gene
•  Column 6: the average end usage for condition 1
•  Column 7: the average end usage for condition 2
•  Column 8: end usage difference. The absolute value of the difference between condition 1 end usage and condition 2 end usage.