PolyA_clip

NAME

polyA_clip -- Mark polyA and polyT heads and tails.

SYNOPSIS

polyA_clip [-vt] [-t] [-x min_length(0)] [p percent_cutoff(95)] [w window_length(50)] files...

OPTIONS

-v

Enable verbose output. This outputs information on which files are currently being clipped.

-t

Test mode. The SL and SR information is written to stdout instead of being appended to the Experiment file.

-x min_length

Sequences which after clipping are shorter than min_length are reported.

-w window_length

The length of the window that is slid along the sequence to analyse the composition.

-p percentage

Windows containing this percentage of A or T bases are considered as polyA or polyT

DESCRIPTION

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 ALSO

See section ExperimentFile(4).