TBtools-Manual

Start a project to make a useful and readable manual for TBtools.

Functions:what TBtools can do?

TBtools, short for "Tools for Biologist", is a Toolset and also a project.
From the very beginning, I just want to develop a Toolset, which can be useful for my self in Command LIne mode, and for my colleage in Graphics User Interface mode.
However, some friends saw this work and said TBtools would also be useful to them. So, I post it on web. And consequently, more and more friends send me feature calls and more and more functions were added into TBtools.
Thus, Tills now(2017/06/29), TBtools as less contains functions as bellowed:

In CLI Mode:

To run TBtools in CLI mode,

• if the running environment has no graphics device, like under terminal to server, just type java -jar TBtools_vX.XX.jar, and then all available tools will be shown. Copy the command for specific tools and use it.
• if the running environment has graphics device, like under windows, mac or X-windows, just type java -jar TBtools_vX.XX.jar anyString... If no string after, then TBtools will try to run in GUI mode and in many cases, a TBtools main windows will shown.

List of Tools under CLI Mode will add in the furture...

In GUI Mode:

To runu TBtools in GUI mode, If the .jar file has been linked to java, then just Double-click the .jar file. the TBtools main window will show up.
If user install TBtools from .exe file under windows, just run TBtools like many other software.
If user want to run TBtools in GUI mode with useful debug information, just type java -jar TBtools_vX.XX.jar debug.

List of Tools under GUI Mode

• Sequence Toolkits

  • Amazing Fasta Extractor
    Transformat Fasta file, make a Fasta-Index and extract Fasta Record in a very quick way.
  • Fasta Stater
    Stat a Fasta file, which can generate a summary information (record counts, total Len, N50, GC contents ...) of all Fasta record and a file contain sequence features (simplified ID, length, GC content ...) of each fasta record.
  • Fasta Extractor
    Directly extract Fasta record from fasta file, which might be slower than Amazing Fasta Extractor... This function will be decrepeted or updated... Recommand use Amazing Fasta Extractor instead.
  • Fasta Subseq
    Similar to Fasta Extractor, however, this function was developed for extract Sequence Region of specific Fasta records... This function will ne decrepeted or updated... Recommand Use Amazing Fasta Extractor instead.
  • Fasta Merge and Split
    Merge several fasta file into one fasta file Or Split one fasta file into several fasta files.
  • Sequence Manipulator
    Tranformat, Reverse, Complement of sequence
  • NCBI Seq Downloader
    Batch download Sequnces from NCBI according to GI or Accession Number list.
  • Get Completes ORF(Open Reading Frame)
    Predict complete ORF from input sequence. At present, this function only detect complete ORF and only the classic codon usage table. That is, a complete ORF here only refer to sequence region starts from ATG and ends with TGA,TAA and TAG.
  • Check Primers(Simple PCR)
    Directly check the primers sequence location to simply stat the specifity of input primer in the specific sequnce database, such as the transcriptome of one species.
  • GFF/GTF Sequence Extractor
    Extractor Sequences from genome according to gene structure annotation file(.gff/.gtf).

• Blast

  • Remote Blast(No Need for Preinstalled Blast)
    Conduct remote blast through NCBI Blast API...This funtion is not stable now, because JRE1.6 doesn't support SSL protocol and I do not want to add third party library for this. Will be updated later.
  • Auto Blast Several Sequences To a Big File[Commonly Used]
    Invoke Blast in the environment to compare several sequences to a big in Fasta format.
  • Auto Blast Two Sequence Sets
    Like above.
  • Auto Blast Two Sequence Sets -Big File-
    Like above. This three functions will be merged into one in the feature.
  • Blast Several Seq To FastQ
    Build a blast database from input fastQ file and Blast several Seq onto it.
  • Reciprocal Blast
    Conduct reciprocal Blast between two input file in fasta format.
  • Blast XML Alignment Shower
    Make a alignment graph of blast result, which can be used to check the coverage of query sequence or subject sequence.
  • Blast XML Dotpot
    Make a dot plot graph of blast result.
  • Blast Pileup Grapher
    Make a pileup graph of blast result, which is similar to NCBI blast web serveive result page.
  • TransFormat Blast.xml to TBtools.table
    TBtools has definded a tab-seperated format to store and descript the blast result. This table contains some useful staticstic info, like weighted-Cov.
  • TransFormat Blast.xml to Blast Table
    This function just transformat the blast xml file to a tab-delimed file also the same as the default blast+ outfmt-6.
  • e-GenomeWalkiing or e-Race
    Use a sequnce to FISH ovelapping reads and assemble into a long sequence. This function might be useful to conduction Genome-walking on Re-sequencing data or 5'RACE or 3'RACE on RNAsequencing data in silco.

• GO and KEGG

  • GO Annotation
    Conduct a gene-ontology annotation. This function is only a ID-mapping tools, which map the input GI,Accession Number of NCBI,Uniprot or Tremble to GO ID.
  • GO Enrichment
    Conduct gene-ontology term enrichment analysis basing on hypergeometrix distribution.
  • GO Level Counter
    Count gene number at specific GO level, output a statistics table and an optional graph.
  • GO Level Compare
    Compare two GO annotation result on specific GO level and output a graph. This function do not work well now. Will fix it.
  • GO Term Parser
    Parse GO annotation, from which user can know every gene2GO and GO2gene mapping information.
  • Prepare GO Annotation for BiNGO in cytoscape
    Transformat many gene-ontology annotation into a formated file for BiNGO.
  • KEGG Enrichment Analysis
    Conduct KEGG pathway analysis basing on hypergeometrix distribution.
  • KEGG Pathwat Map Drawer
    Hightlight genes on KEGG pathway map.

• Other

  • Color Picker
    Pick color code freely and save color code graph as needed.
  • Table ID Manipulator
    Extract, Filter or Rank table Row
  • Table Column Manipulator
    Rank or keep only Column selected... Extract or Filter funstion WILL BE ADDED.
  • Big Text Viewer
    Take a glance of text file with very Big Size in a very quick way.
  • Big Table Viewer
    Take a glance of table file with very Big Size in a very quick way.
  • Text Block Extractor
    Extract Text Block with specific ID list and record seperate string. This function was developed for extracting synteny block.
  • Expression Shower
    Visulize expression trend of one gene or several gene.
  • Expression Calculator
    Calculate expression value (RPKM or TPM value) according gene.counts and gene.len
  • Wonderful Venn (Up to Six Sets)
    Conduct Venn analysis in an interative way.
  • Map Genes On Genome From Sequence Files
    Conduct Blast to get the positon region of input gene on genome and then output a graph
  • Map Genes On Genome From Position Info File
    Draw a gene on genome file basing on input gene and genome info.
  • Dual Synteny Plot from MCScanX output
    Visulize result from MCScanX in a interactive way.
  • Domain/Motif Pattern Drawers
    Visulzie result from MEME suite, NCBI Batch-CD search, pfam-search or GFF/GTF.

• About

  • About TBtools
    Show some information about TBtools.
  • Debug Dialog
    Show Debug dialog, which could be used for bugs tracking.
  • Resize JVM Memory
    Some functions need high memory. So, this function could be used to get a new TBtools Windows wich higher memory. It may be failed under some environment.

Usage:how to use TBtools?

A very very long way to go...

FAQs:why TBtools fails?

1. Sequence extraction failed.
   Most of the time, if TBtools fail to extract sequences from fasta file, the reason should the *Input ID List* is not match in the *Subject Fasta File*. Test it.
2. Blast-related Functions failed.
   Thest function has been test for a many many times by many many friends, they should have been statble and robust for quite a long time. If TBtools faided in these function, please check whether the *blast* could be normally run in Command line environment.
...

Bugs:where to report the bugs and help developing TBtools?

There are many ways to *report bugs* and send *feature calls* for TBtools:

• Send Me an email: ccj0410@gmail.com
• Through QQ chatting group: TBools使用交流群(553679029) ...

To Updates:

• Fasta Extractor
• Fasta Subseq
• Fasta Split

To DO:

• Seven set and Eight set Venn