F-Seq

Tag sequencing using high-throughput sequencing technologies are now regularly employed to identify specific sequence features such as transcription factor binding sites (ChIP-seq) or regions of open chromatin (DNase-seq). To intuitively summarize and display individual sequence data as an accurate and interpretable signal, we developed F-Seq, a software package that generates a continuous tag sequence density estimation allowing identification of biologically meaningful sites whose output can be displayed directly in the UCSC Genome Browser.

more info

article: F-Seq: a feature density estimator for high-throughput sequence tags
online manual: http://fureylab.web.unc.edu/software/fseq/

# command arguments

F-Seq Version 1.81
usage: fseq [options]... [file(s)]...
-b <background dir>     background directory (default=none)
-d <input dir>          input directory (default=current directory)
-f <arg>                fragment size (default=estimated from data)
-h                      print usage
-l <arg>                feature length (default=600)
-o <output dir>         output directory (default=current directory)
-of <wig | bed | npf>   output format (default wig)
-p <ploidy dir>         ploidy/input directory (default=none)
-s <arg>                wiggle track step (default=1)
-t <arg>                threshold (standard deviations) (default=4.0)
-v                      verbose outputNote: DNase HS data (5' ends) - set -f 0

# A perl script has been included which converts data from mapview format (MAQ alignment results) to BED format.

Usage:  mapviewToBed.pl <MIN QUAL> <MAX_HITS> <FILE>
 MIN_QUAL        = Exclude alignments with <= this mapping quality score.
 MAX_HITS        = Exclude alignments with > this number of hits.
 FILE            = Mapview file to convert.

Example: perl mapviewToBed.pl 0 2 sequence.mapview

This takes as input sequence.mapview, only uses sequences aligning in fewer than 2 locations with 0 or 1 mismatches, and only sequences with an alignment score of 0 or better.