[{"_1":2,"_175":-5,"_176":-5},"loaderData",{"_3":4,"_17":18,"_25":26,"_150":151},"root",{"_5":-5,"_6":-7,"_7":8,"_9":-7,"_10":11,"_12":-7,"_13":14,"_15":16},"currentUser","primaryEmail","siteVerification","6LeIxAcTAAAAAJcZVRqyHh71UMIEGNQ_MXjiZKhI","toast","enableDev",false,"incidentStatus","theme","system","contrast","normal","routes/_layout",{"_19":-5,"_20":21,"_22":21,"_23":11,"_24":21},"username","isAskGordonEnabled",true,"isUsingNewTemplate","showMinimalLanding","showHoneypotTrap","routes/_layout.r.$namespace.$reponame",{"_27":28,"_29":-5,"_30":11,"_31":11,"_32":33,"_34":35,"_36":-5,"_37":11,"_38":39,"_88":-5,"_89":90,"_139":-5,"_140":11,"_141":21,"_142":11,"_143":-5,"_144":11,"_145":-5,"_146":147,"_148":91,"_149":-7},"canonicalUrl","https://hub.docker.com/r/rluis/baminsight/tags","mcpServer","canSeeDockerfile","canSeeAutobuilds","namespace","rluis","reponame","baminsight","cloudBuildSource","isAutobuildsAvailable","repo",{"_40":41,"_42":43,"_45":46,"_47":48,"_49":11,"_50":51,"_52":53,"_54":55,"_57":35,"_32":33,"_58":59,"_60":44,"_61":62,"_63":64,"_65":66,"_67":-5,"_68":62,"_69":70,"_71":11,"_72":33,"_73":74,"_79":21,"_80":81,"_85":33,"_86":87},"categories",[],"content_types",[44],"image","date_registered","2017-12-13T15:38:11.372702Z","description","A Useful bioinformatic tool to quickly vizualize your BAM files in Genome Browser UCSC","is_private","last_updated","2021-10-07T13:07:07.412907Z","last_modified","2024-10-16T13:48:34.145251Z","media_types",[56],"application/vnd.docker.container.image.v1+json","name","pull_count",1032,"repository_type","star_count",0,"status",1,"status_description","active","source","collaborator_count","full_description","# BamInsight\n\n![GitHub package](https://img.shields.io/badge/BamInsight-v1.1-green.svg)\n[![Language](http://img.shields.io/badge/Language-Python-yellow.svg)](https://www.python.org/)\n[![BSD license](https://img.shields.io/badge/License-BSD_3_Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause)\n[![DockerHub](https://img.shields.io/badge/Docker-maintained-blue.svg)](https://hub.docker.com/r/rluis/baminsight/)\n\nA Useful bioinformatic tool to quickly vizualize your data in Genome Browser UCSC. We don't want to reinvent the wheel. We just want to simplify it.\n\n\nTable of Contents\n=================\n\n* [Installation](#installation)\n * [Classical Installation](#classical-installation)\n * [Docker Image Usage](#docker-image)\n* [Usage](#usage)\n * [Baminsight Stranded Mode](#baminsight-stranded-mode)\n * [Baminsight Original Mode](#baminsight-original-mode)\n* [Contact](#contact)\n \n## Installation\n\n\n### Classical Installation \n\nType the following commands to install BamInsight:\n\n```\npython setup.py build\npython setup.py install \n```\n\nPlease ensure you have installed the python packages refered below:\n\n* [Pandas](https://pandas.pydata.org/)\n* [Pybedtools](https://daler.github.io/pybedtools/)\n* [PyBigWig](https://github.com/deeptools/pyBigWig)\n* [Pysam](https://github.com/pysam-developers/pysam/blob/master/doc/index.rst)\n* [Setuptools](https://pypi.org/project/setuptools/)\n\n### Docker Image Usage\n\nUse of our docker image can be a more user-friendly way to have a bamInsight experience:\n\n```\n(sudo) docker pull rluis/baminsight\n```\n\nThere are already inside all the necessary packages to run the software. \n\n# Usage\n\nVisualization of NGSs reads of some genes is a good\nform to understand the dataset you have on hands \n([A survey of best practices for RNA-seq data analysis][1]).\n\nOne of the most popular genome viewer is [UCSC Genome Browser][2]. \nIt is very flexible it terms of data input and allow link share of sessions, which facititates \nthe brainstorm and let a interesting interface between dry and wet lab researchers. \n\nHowever, from the moment you have the bam file ready, to the point where you visualize \ntypical bam coverage, It takes some time, which sometimes discourage some bioinformaticians,\npushing on some mistakes that could be visualize directly in a genome viewer.\n\nSome files can directly be loaded to [UCSC Genome Browser][2] (file size < 500 Mb). However, in the majority\nof the times, It is necessary to prepare side files to be interpreted by Genome Browser. \n\nIn that way, We decided to create BamInsight Software. A software that makes by you the annoying \npart from a bam file to visualize your dataset in UCSC genome Browser, dealing with all intermediate \nfiles and bridging the gap existing right now.\n\n### Baminsight Stranded Mode\n\nIf your dataset is Stranded (RNA-seq fr-firstranded, fr-secondsetranded, or other), \nyou should use this baminsight mode to visualize on genome browser one track with forward and reverse\nreads coverage, representing plus and minus (also known as Watson and Crick) strands, respectively.\n\nExample Command:\n ```\nbaminsight stranded hg38 ruisergiolusi@gmail.com Rnaseq_rep1_HelaS3.bam -FF 83,163 -FR 99,147 -add_bam -FTPHOST yourftp.hostname.com \n-FTPUser ftpusername -FTPPassword ultrasecretpassword -FTPPort 21 -FTPPath /path/to/be/allocated/baminsight/output \n-long_label HelaS3_Rep1 -short_label HeLa1 \n```\n\nPicture below sum-up this mode.\n\n![alt text](Configs/Pictures/workflow_Stranded.png)\n\nFistly, there is three positional arguments for baminsight:\n\n* **mode** - (original or **stranded**) (_stranded in this mode_)\n* **genome** - (example - hg38 or mm10, etc) (_genome necessary files are downloaded during \nbaminsight execution. So even less known assembled genomes work in baminsight ;)_)\n* **email** - (your email - It is used to input your data in UCSC Genome Browser)\n\nEvery command in stranded mode has to begin as:\n```\nbaminsight stranded (genome) (email) ...\n\nbaminsight stranded hg38 ruisergiolusi@gmail.com ...\nor\nbaminsight stranded mm10 ruisergiolusi@gmail.com ...\n```\nYou have to give to bamInsight one (or more) bam file(s), and the flags according to your dataset's\nstrandness. [A endless book of doubts can be arise of this topic][3], but the following \ntable can resume it:\n\n| Strandeness Type | Flags to use |\n| ------------- | ------------- |\n| fr-firststrand | -FF 83,163 -FR 99,147 |\n| fr-secondstranded | -FF 99,147 -FR 83,163 |\n| fr-unstranded | USE Baminisht Original MODE (described below) |\n\nIf you don't know your dataset strandness, run [infer_experiment.py][4] from RSeQC. \n\n```\n[FR-FIRSTRAND]\nbaminsight stranded (genome) (email) --names bamfile1.bam bamfile2.bam -FF 83,163 -FR 99,147 \n\nbaminsight stranded hg38 ruisergiolusi@gmail.com Rnaseq_rep1_HelaS3.bam Rnaseq_rep2_HelaS3.bam -FF 83,163 -FR 99,147 \n\n[FR-SECONDSTRAND]\nbaminsight stranded (genome) (email) --names bamfile1.bam bamfile2.bam -FF 99,147 -FR 83,163 \n\nbaminsight stranded hg38 ruisergiolusi@gmail.com Rnaseq_rep1_HelaS3.bam Rnaseq_rep2_HelaS3.bam -FF 99,147 -FR 83,163 \n```\n\nIt is possible to directly visualize the bam reads in [UCSC Genome Browser][2]. For that just \nadd to bamInsight the argument _-addbam_ .\n\n```\nbaminsight stranded hg38 ruisergiolusi@gmail.com Rnaseq_rep1_HelaS3.bam Rnaseq_rep2_HelaS3.bam -FF 83,163 -FR 99,147 -add_bam\n```\n\nFinally, It is possible to directly send the final directory containing bigWig and auxiliary files,\nto your own FTP server. It is the last step before you visualize your dataset in the genome viewer.\nFor that you just need to define FTP host name, username, password, port and path just as indicated\nbelow:\n\n ```\nbaminsight stranded hg38 ruisergiolusi@gmail.com Rnaseq_rep1_HelaS3.bam -FF 83,163 -FR 99,147 -add_bam -FTPHOST yourftp.hostname.com \n-FTPUser ftpusername -FTPPassword ultraSecretPassword -FTPPort 21 -FTPPath /path/to/be/allocated/baminsight/output\n```\n\nIf you want to re-define the names of the final tracks please use the _-long_label_ or/and _-short_label_ arguments.\nOtherwise, tracks names will be equal as bam file names.\n\n\n\n#### Upload Output Files to UCSC Genome Browser \n\nBaminsight work reach the end. Now is just follow the next few steps to upload the all\nfiles generated in bamInsight, to [UCSC Genome Browser][2].\n\n\n##### STEP 1\n\n**1** - On a web browser open [UCSC Genome Browser][2] website - https://genome-euro.ucsc.edu/.\n\n**2** - Click on _**My Data**_ > _**MySessions**_ .\n \n\n![alt text](Configs/Pictures/BG1_explained.png)\n\n##### STEP 2\n\n**3** - Create a UCSC account. If you have have just Login.\n\n![alt text](Configs/Pictures/GB2_explained.png)\n\n##### STEP 3\n\n**4** - Click on _**Track Hubs**_\n\n![alt text](Configs/Pictures/GB3_explained.png)\n\n##### STEP 4\n\n**5** - Select _**My Hubs**_.\n\n**6** - Paste the link on _**URL**_ formed as:\n\n```\nftp://:@:/hub.txt\nftp://ftpusername:ultraSecretPassword@yourftp.hostname.com:21/path/to/be/allocated/baminsight/output/hub.txt\n```\n\nEnd the process clicking on Add Hub.\n\n**7** - Visualize your track in clicking on _**Genome Browser**_\n\n![alt text](Configs/Pictures/GB4_explained.png)\n\n\n### Baminsight Original Mode\n\n_**bamInsight Original**_ Mode only differ from _**Stranded Mode**_ in the first part of the process.\nwhile Stranded mode divide the given bam file in forward and reverse reads, this mode keep \nthe file as the _Original_, as can be seen in the next picture. \n\n![alt text](Configs/Pictures/workflow_Original.png)\n\nThen, It is presented a example command:\n\n ```\nbaminsight original hg38 ruisergiolusi@gmail.com Chipseq_rep1_HelaS3.bam -add_bam -FTPHOST yourftp.hostname.com \n-FTPUser ftpusername -FTPPassword ultrasecretpassword -FTPPort 21 -FTPPath /path/to/be/allocated/baminsight/output \n-long_label HelaS3_Rep1 -short_label HeLa1 \n```\n\n# Contact\nI hope bamInsight could be so useful for you, than It is for me, in your bioinformatic daily tasks. \nFor more information, or in case of any doubt please open a new issue in github or send \nme a [private message](mailto:ruisergioluis@gmail.com).\n\n\n[1]:https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0881-8\n[2]:https://genome-euro.ucsc.edu/\n[3]:https://www.biostars.org/p/169942/\n[4]:https://github.com/dnanexus/rseqc/blob/master/rseqc/scripts/infer_experiment.py \n","has_starred","hub_user","immutable_tags_settings",{"_75":11,"_76":77},"enabled","rules",[78],".*","is_automated","permissions",{"_82":21,"_83":11,"_84":11},"read","write","admin","user","storage_size",7829815009,"orgData","recentTags",[91,129],{"_92":44,"_93":94,"_95":96,"_97":98,"_99":100,"_50":118,"_119":94,"_120":33,"_121":56,"_57":122,"_123":124,"_125":109,"_126":118,"_127":66,"_128":21},"content_type","creator",2327310,"full_size",526250581,"id",19368835,"images",[101],{"_102":103,"_104":105,"_106":107,"_108":109,"_110":111,"_112":113,"_114":107,"_115":-5,"_116":96,"_63":66,"_117":-5},"architecture","amd64","digest","sha256:c50ba13009f03a1a17f6a9346f9872bde8e240468432bf5cb43e52bd6b6bd88a","features","","last_pulled","2026-10-04T19:15:25.876639835Z","last_pushed","2019-06-05T10:54:29Z","os","linux","os_features","os_version","size","variant","2021-10-07T13:07:07.114843Z","last_updater","last_updater_username","media_type","latest","repository",2405050,"tag_last_pulled","tag_last_pushed","tag_status","v2",{"_92":44,"_93":94,"_95":130,"_97":131,"_99":132,"_50":137,"_119":94,"_120":33,"_121":56,"_57":138,"_123":124,"_125":135,"_126":137,"_127":66,"_128":21},529873130,26520252,[133],{"_102":103,"_104":134,"_106":107,"_108":135,"_110":136,"_112":113,"_114":107,"_115":-5,"_116":130,"_63":66,"_117":-5},"sha256:e5f16f165372099cec3de4faf114f44d1d00c6b20acb9c5b94f9bb0c572c190a","2026-10-08T22:35:31.92003918Z","2018-11-15T03:08:49Z","2018-11-15T03:08:48.850563Z","dev","sbxKitMetadata","isPotentialSpam","isHubSbxKitsEnabled","showSbxLogoOverride","sbxTrademarkText","displaySecurityMetadata","tagAttestations","tagsHaveAttestations",[],"selectedTag","attestationsUrl","routes/_layout.r.$namespace.$reponame.tags",{"_38":152,"_159":160,"_146":173,"_174":11},{"_40":153,"_42":154,"_45":46,"_47":48,"_49":11,"_50":51,"_52":53,"_54":155,"_57":35,"_32":33,"_58":59,"_60":44,"_61":62,"_63":64,"_65":66,"_67":-5,"_68":62,"_69":70,"_71":11,"_72":33,"_73":156,"_79":21,"_80":158,"_85":33,"_86":87},[],[44],[56],{"_75":11,"_76":157},[78],{"_82":21,"_83":11,"_84":11},"tags",{"_161":162,"_163":-5,"_164":-5,"_165":166},"count",2,"next","previous","results",[167,170],{"_92":44,"_93":94,"_95":96,"_97":98,"_99":168,"_50":118,"_119":94,"_120":33,"_121":56,"_57":122,"_123":124,"_125":109,"_126":118,"_127":66,"_128":21},[169],{"_102":103,"_104":105,"_106":107,"_108":109,"_110":111,"_112":113,"_114":107,"_115":-5,"_116":96,"_63":66,"_117":-5},{"_92":44,"_93":94,"_95":130,"_97":131,"_99":171,"_50":137,"_119":94,"_120":33,"_121":56,"_57":138,"_123":124,"_125":135,"_126":137,"_127":66,"_128":21},[172],{"_102":103,"_104":134,"_106":107,"_108":135,"_110":136,"_112":113,"_114":107,"_115":-5,"_116":130,"_63":66,"_117":-5},[],"canDeleteTags","actionData","errors"]

rluis/baminsight

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