Tools

All scripts are located in ./workflow/scripts.

Step 1

• count_junctions.py - extracts splice junctions from alignment file (BAM) with their read counts.

• count_sites.py - extracts splice sites with only continuous reads support from alignment file (BAM).

Step 2

• aggregate_junctions.py - aggregates read counts for junctions from the first step (J1). Adds strand information to junctions and filters out junctions if their corresponding introns are too short or too long.

• aggregate_sites.py - aggregates read counts for sites from the first step (S1/PS1).

Step 3

• annotate_junctions.py - retrieves splice site sequences for aggregated junctions from the second step (J2). Adds their annotation status.

Step 4

• choose_strand.py - chooses correct strand for each junction from the third step (J3).

Step 6

• filter.py - filters junctions or sites from previous steps by various criteria.

Step 7

• compute_rates.py

Auxiliary

• describe_replicates.py

• merge_junctions.py