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A Feature Density Estimator for High-Throughput Sequence Tags
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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. 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.
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A Feature Density Estimator for High-Throughput Sequence Tags
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