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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 dir> background directory (default=none) -c <arg> genomic count of sequence reads (defualt = calculated) -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 output -wg <arg> 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/>.