PureCLIPs output

Crosslink sites

The main output of PureCLIP is a BED6 file containing individual crosslink sites associated with a score:

1. chr: Name of the chromosome or scaffold.
2. start: Position of crosslink site.
3. end: Position behind crosslink site (start+1).
4. state: ‘3’ (0-based, corresponds to state ‘4’ in the PureCLIP publication)
5. score: log posterior probability ratio of the first and second likely state.
6. strand: + or -

Binding regions

Optionally, if an output file for binding regions is specified with -or, individual crosslink sites with a distance <= d (specified with -dm, default 8 bp) are merged and given out in a separate BED6 file:

1. chr: Name of the chromosome or scaffold.
2. start: Start position, position of first crosslink site.
3. end: End position, position behind last crosslink site.
4. indiv. scores: ‘score1;score2;score3;’
5. score: Sum of log posterior probability ratio scores.
6. strand: + or -