https://github.com/aboyle/F-seq

A Feature Density Estimator for High-Throughput Sequence Tags
https://github.com/aboyle/F-seq

Last synced: 26 days ago
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A Feature Density Estimator for High-Throughput Sequence Tags

• Host: GitHub
• URL: https://github.com/aboyle/F-seq
• Owner: aboyle
• License: gpl-3.0
• Created: 2011-06-13T20:58:48.000Z (over 13 years ago)
• Default Branch: master
• Last Pushed: 2021-05-25T14:49:50.000Z (over 3 years ago)
• Last Synced: 2024-02-14T03:31:20.520Z (10 months ago)
• Language: Java
• Homepage: http://fureylab.web.unc.edu/software/fseq/
• Size: 78.1 KB
• Stars: 23
• Watchers: 3
• Forks: 5
• Open Issues: 6
• Metadata Files:
  • Readme: README.txt
  • License: LICENSE

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• Awesome-Bioinformatics-Benchmarks - F-seq

README

        
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    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 .