{"id":13773736,"url":"https://github.com/aboyle/F-seq","last_synced_at":"2025-05-11T06:30:32.805Z","repository":{"id":74587503,"uuid":"1891080","full_name":"aboyle/F-seq","owner":"aboyle","description":"A Feature Density Estimator for High-Throughput Sequence Tags","archived":false,"fork":false,"pushed_at":"2021-05-25T14:49:50.000Z","size":80,"stargazers_count":23,"open_issues_count":6,"forks_count":5,"subscribers_count":3,"default_branch":"master","last_synced_at":"2024-02-14T03:31:20.520Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"http://fureylab.web.unc.edu/software/fseq/","language":"Java","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/aboyle.png","metadata":{"files":{"readme":"README.txt","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2011-06-13T20:58:48.000Z","updated_at":"2024-02-14T03:31:20.520Z","dependencies_parsed_at":"2023-02-27T03:01:29.130Z","dependency_job_id":null,"html_url":"https://github.com/aboyle/F-seq","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/aboyle%2FF-seq","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/aboyle%2FF-seq/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/aboyle%2FF-seq/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/aboyle%2FF-seq/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/aboyle","download_url":"https://codeload.github.com/aboyle/F-seq/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":225017829,"owners_count":17407835,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-08-03T17:01:19.565Z","updated_at":"2024-11-17T08:31:28.334Z","avatar_url":"https://github.com/aboyle.png","language":"Java","funding_links":[],"categories":["DNase, ATAC, and ChIP-seq"],"sub_categories":["Peak Callers"],"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\n\nWelcome to F-Seq.\n\nThis software requires Java version 1.5 or greater.  \nTo see your version of java (or if it is installed), type 'java -version'\n\nIf java is not installed or you do not have the correct version, download at \nhttp://java.sun.com/javase/downloads/index.jsp\n\nCurrent accepted input formats:\nBed, http://genome.ucsc.edu/FAQ/FAQformat#format1\n\nCurrently accepted output formats:\nWiggle, http://genome.ucsc.edu/FAQ/FAQformat#format6\nBed (see above)\n\n-----------------------------------\nUnix (Linux)\n\nBuild with ant from the base directory:\n~$ git clone https://github.com/aboyle/F-seq.git\n~$ cd F-seq/\n~/F-seq$ ant\n\nThis will build F-seq and package it in the dist~ folder. To then run F-seq:\n~/F-seq$ cd dist~/\n~/F-seq/dist~$ tar -xvf fseq.tgz\n~/F-seq/dist~$ cd fseq/bin/\n~/F-seq/dist~/fseq/bin$ ./fseq\nF-Seq Version 1.85\nusage: fseq [options]... [file(s)]...\n -b \u003cbackground dir\u003e     background directory (default=none)\n -c \u003carg\u003e                genomic count of sequence reads (defualt =\n                         calculated)\n -d \u003cinput dir\u003e          input directory (default=current directory)\n -f \u003carg\u003e                fragment size (default=estimated from data)\n -h                      print usage\n -l \u003carg\u003e                feature length (default=600)\n -o \u003coutput dir\u003e         output directory (default=current directory)\n -of \u003cwig | bed | npf\u003e   output format (default wig)\n -p \u003cploidy dir\u003e         ploidy/input directory (default=none)\n -s \u003carg\u003e                wiggle track step (default=1)\n -t \u003carg\u003e                threshold (standard deviations) (default=4.0)\n -v                      verbose output\n -wg \u003carg\u003e               wg threshold set (defualt = calculated)\n \n\nMake sure 'bin/fseq' is executable (chmod 0755 bin/fseq)\n\nFor a list of options, type 'fseq -h'\n\nExample: fseq -v -of wig chr1.bed chr2.bed\n\nThis takes as input the chr1.bed and chr2.bed files. \nWill use verbose output and outputs the densities in the wiggle format.\n\n-----------------------------------\nTroubleshooting\n\nA likely cause for errors is an \"OutOfMemory\" exception.  \nTo increase the available memory to the java virtual machine, edit\n'bin/fseq' file and change the JAVA_OPTS property to increase the heap size.\n\nUsers also typically complain about an 'ArrayOutOfBounds' exception. This is due to a low number of reads\nand is fixed in the latest version of F-seq. You can also get around this error by using the -f option\nto set your fragment size.\n\n-----------------------------------\nLicense\n\nLicensed under the GNU General Public License 3.0 license.\n\nF-seq is free software: you can redistribute it and/or modify\nit under the terms of the GNU General Public License as published by\nthe Free Software Foundation, either version 3 of the License, or\n(at your option) any later version.\n\nF-seq is distributed in the hope that it will be useful,\nbut WITHOUT ANY WARRANTY; without even the implied warranty of\nMERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\nGNU General Public License for more details.\n\nYou should have received a copy of the GNU General Public License\nalong with F-seq.  If not, see \u003chttp://www.gnu.org/licenses/\u003e.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Faboyle%2FF-seq","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Faboyle%2FF-seq","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Faboyle%2FF-seq/lists"}