polyA_clip -- Mark polyA and polyT heads and tails.
p percent_cutoff(95)] [
w window_length(50)] files...
PolyA_clip searches the 5' and 3' ends of sequence readings for the presence of polyA and polyT heads and tails. It marks them using the SL and SR experiment file records, and hence should be applied after quality clipping and sequence vector clipping. Any number of files can be processed in a single run. The algorithm is as follows. The user supplies window_length and percentage. From MIN(QR,SR) slide the window left until percent_A < percentage and percent_T < percentage. Then from the right edge of the window look left until a C or G is found. Mark this base SR. Do the equivalent for the 5' end and mark SL.
See section ExperimentFile(4).