F-seq

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F-seq is deprecated. Please see F-seq 2 for a more modern implementation of this tool: https://github.com/Boyle-Lab/F-Seq2

Welcome to F-Seq.

This software requires Java version 1.5 or greater.
To see your version of java (or if it is installed), type 'java -version'

If java is not installed or you do not have the correct version, download at http://java.sun.com/javase/downloads/index.jsp

Current accepted input formats: Bed, http://genome.ucsc.edu/FAQ/FAQformat#format1

Currently accepted output formats: Wiggle, http://genome.ucsc.edu/FAQ/FAQformat#format6 Bed (see above)

Unix (Linux)

Build with ant from the base directory: ~$ git clone https://github.com/aboyle/F-seq.git ~$ cd F-seq/ ~/F-seq$ ant

This will build F-seq and package it in the dist~ folder. To then run F-seq: ~/F-seq$ cd dist~/ ~/F-seq/dist~$ tar -xvf fseq.tgz ~/F-seq/dist~$ cd fseq/bin/ ~/F-seq/dist~/fseq/bin$ ./fseq F-Seq Version 1.85 usage: fseq [options]... [file(s)]... -b background directory (default=none) -c genomic count of sequence reads (defualt = calculated) -d input directory (default=current directory) -f fragment size (default=estimated from data) -h print usage -l feature length (default=600) -o

output directory (default=current directory) -of <wig | bed | npf> output format (default wig) -p ploidy/input directory (default=none) -s wiggle track step (default=1) -t threshold (standard deviations) (default=4.0) -v verbose output -wg wg threshold set (defualt = calculated)

Make sure 'bin/fseq' is executable (chmod 0755 bin/fseq)

For a list of options, type 'fseq -h'

Example: fseq -v -of wig chr1.bed chr2.bed

This takes as input the chr1.bed and chr2.bed files. Will use verbose output and outputs the densities in the wiggle format.

Troubleshooting

A likely cause for errors is an "OutOfMemory" exception.
To increase the available memory to the java virtual machine, edit 'bin/fseq' file and change the JAVA_OPTS property to increase the heap size.

Users also typically complain about an 'ArrayOutOfBounds' exception. This is due to a low number of reads and is fixed in the latest version of F-seq. You can also get around this error by using the -f option to set your fragment size.

License

Licensed under the GNU General Public License 3.0 license.

F-seq is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

F-seq is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with F-seq. If not, see http://www.gnu.org/licenses/.