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iimogiimog
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added a basic tutorial to demonstrate data import into tbro with example data
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‎doc/tutorial/protocol_f2.aux‎

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\relax
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\abx@aux@sortscheme{none}
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\@writefile{toc}{\boolfalse {citerequest}\boolfalse {citetracker}\boolfalse {pagetracker}\boolfalse {backtracker}\relax }
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\@writefile{lof}{\boolfalse {citerequest}\boolfalse {citetracker}\boolfalse {pagetracker}\boolfalse {backtracker}\relax }
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\@writefile{lot}{\boolfalse {citerequest}\boolfalse {citetracker}\boolfalse {pagetracker}\boolfalse {backtracker}\relax }
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\select@language{english}
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\@writefile{toc}{\defcounter {refsection}{0}\relax }\@writefile{toc}{\select@language{english}}
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\@writefile{lof}{\defcounter {refsection}{0}\relax }\@writefile{lof}{\select@language{english}}
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\@writefile{lot}{\defcounter {refsection}{0}\relax }\@writefile{lot}{\select@language{english}}
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\abx@aux@cite{CSATIVA}
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\abx@aux@cite{DIP_TBRO}
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\@writefile{toc}{\contentsline {section}{\numberline {1}Introduction}{2}}
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\@writefile{toc}{\contentsline {section}{\numberline {2}Data}{2}}
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\@writefile{toc}{\contentsline {subsection}{\numberline {2.1}Cannabis sativa}{2}}
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\@writefile{toc}{\contentsline {section}{\numberline {3}Bringing the data into TBro}{2}}
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\@writefile{lot}{\contentsline {table}{\numberline {1}{\ignorespaces Programs used for analyses}}{3}}
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\newlabel{tab:PROGRAMS}{{1}{3}}
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\@writefile{toc}{\contentsline {subsection}{\numberline {3.1}The Cannabis sativa transcriptome}{3}}
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\@writefile{toc}{\contentsline {subsubsection}{\numberline {3.1.1}Preparation}{3}}
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\@writefile{toc}{\contentsline {subsubsection}{\numberline {3.1.2}The Transcripts}{3}}
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\@writefile{toc}{\contentsline {subsubsection}{\numberline {3.1.3}Predicted Peptides}{4}}
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\@writefile{toc}{\contentsline {subsubsection}{\numberline {3.1.4}RepeatMasker}{5}}
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\@writefile{toc}{\contentsline {subsubsection}{\numberline {3.1.5}Interpro}{6}}
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\@writefile{toc}{\contentsline {subsubsection}{\numberline {3.1.6}Blast2GO}{6}}
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\@writefile{toc}{\contentsline {paragraph}{\nonumberline GO}{7}}
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\@writefile{toc}{\contentsline {paragraph}{\nonumberline EC}{7}}
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\@writefile{toc}{\contentsline {paragraph}{\nonumberline Description}{7}}
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\@writefile{toc}{\contentsline {subsubsection}{\numberline {3.1.7}Mercator}{7}}
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\@writefile{toc}{\contentsline {subsubsection}{\numberline {3.1.8}Expression Counts}{8}}
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\@writefile{toc}{\contentsline {subsubsection}{\numberline {3.1.9}Differential Expression}{11}}
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\@writefile{toc}{\contentsline {subsubsection}{\numberline {3.1.10}Blast DB}{12}}
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\@writefile{toc}{\contentsline {subsubsection}{\numberline {3.1.11}Synonym / Publication}{13}}
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\@writefile{toc}{\contentsline {subsubsection}{\numberline {3.1.12}Pathways}{13}}
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\@writefile{toc}{\contentsline {subsection}{\numberline {3.2}Any other transcriptome}{14}}
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\@writefile{lof}{\contentsline {figure}{\numberline {1}{\ignorespaces Basic information}}{15}}
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\newlabel{fig:basic}{{1}{15}}
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\@writefile{lof}{\contentsline {figure}{\numberline {2}{\ignorespaces Sequence Annotation}}{15}}
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\newlabel{fig:annotation}{{2}{15}}
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\@writefile{lof}{\contentsline {figure}{\numberline {3}{\ignorespaces Predicted peptids}}{16}}
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\newlabel{fig:predpep}{{3}{16}}
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\@writefile{lof}{\contentsline {figure}{\numberline {4}{\ignorespaces GO}}{16}}
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\newlabel{fig:go}{{4}{16}}
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\@writefile{lof}{\contentsline {figure}{\numberline {5}{\ignorespaces EC}}{17}}
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\newlabel{fig:ec}{{5}{17}}
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\@writefile{lof}{\contentsline {figure}{\numberline {6}{\ignorespaces Mapman Mercator}}{17}}
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\newlabel{fig:mapman}{{6}{17}}
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\@writefile{lof}{\contentsline {figure}{\numberline {7}{\ignorespaces RepeatMasker}}{17}}
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\newlabel{fig:repeatmasker}{{7}{17}}
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\@writefile{lof}{\contentsline {figure}{\numberline {8}{\ignorespaces Expression Barplot for a single Isoform}}{18}}
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\newlabel{fig:barplot_iso}{{8}{18}}
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\@writefile{lof}{\contentsline {figure}{\numberline {9}{\ignorespaces Expression Barplot for all isoforms in a cart}}{19}}
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\newlabel{fig:barplot_cart}{{9}{19}}
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\@writefile{toc}{\contentsline {section}{\numberline {4}Exploring the imported Data}{19}}
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\@writefile{toc}{\contentsline {subsection}{\numberline {4.1}Feature annotations}{19}}
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\@writefile{toc}{\contentsline {subsection}{\numberline {4.2}Expressions}{19}}
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\@writefile{toc}{\contentsline {subsection}{\numberline {4.3}Differential Expressions}{19}}
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\@writefile{toc}{\contentsline {subsection}{\numberline {4.4}Carts}{19}}
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\@writefile{toc}{\contentsline {subsection}{\numberline {4.5}Pathways}{19}}
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\@writefile{toc}{\contentsline {subsection}{\numberline {4.6}Searches}{19}}
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\@writefile{toc}{\contentsline {subsection}{\numberline {4.7}Blast}{19}}
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\@writefile{lof}{\contentsline {figure}{\numberline {10}{\ignorespaces Differential expression}}{20}}
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\newlabel{fig:diffexp}{{10}{20}}
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\@writefile{lof}{\contentsline {figure}{\numberline {11}{\ignorespaces Differential expression results Flower vs Leaf}}{21}}
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\newlabel{fig:diffexp_results}{{11}{21}}
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\@writefile{lof}{\contentsline {figure}{\numberline {12}{\ignorespaces Carts}}{22}}
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\newlabel{fig:carts}{{12}{22}}
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\@writefile{lof}{\contentsline {figure}{\numberline {13}{\ignorespaces List of Pathways in the cart}}{23}}
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\newlabel{fig:pathway}{{13}{23}}
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\@writefile{lof}{\contentsline {figure}{\numberline {14}{\ignorespaces Combisearch}}{24}}
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\newlabel{fig:combisearch}{{14}{24}}
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\@writefile{lof}{\contentsline {figure}{\numberline {15}{\ignorespaces Multisearch}}{24}}
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\newlabel{fig:multisearch}{{15}{24}}
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\@writefile{lof}{\contentsline {figure}{\numberline {16}{\ignorespaces Blast interface}}{25}}
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\newlabel{fig:blast}{{16}{25}}
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\@writefile{lof}{\contentsline {figure}{\numberline {17}{\ignorespaces Blast results}}{26}}
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\newlabel{fig:blast_results_1}{{17}{26}}
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\@writefile{lof}{\contentsline {figure}{\numberline {18}{\ignorespaces Blast results}}{27}}
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\newlabel{fig:blast_results_2}{{18}{27}}

‎doc/tutorial/protocol_f2.bbl‎

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{}
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\refsection{0}
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\entry{CSATIVA}{article}{}
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}
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\strng{fullhash}{ab09963863f6859dff959b7b17a01c53}
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\field{sortinit}{0}
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\field{labeltitle}{{The draft genome and transcriptome of Cannabis sativa.}}
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\field{issn}{1465-6914}
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\field{journaltitle}{Genome biology}
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\field{month}{01}
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\field{number}{10}
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\field{title}{{The draft genome and transcriptome of Cannabis sativa.}}
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\field{volume}{12}
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\field{year}{2011}
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\field{pages}{R102}
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\verb{doi}
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\verb 10.1186/gb-2011-12-10-r102
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\verb{url}
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\verb http://genomebiology.com/2011/12/10/R102
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{University of W\"urzburg}%
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\field{labeltitle}{{Visualizing denovo RNAseq experiments - Creating a toolchain for storage, visualization and comparison of RNA expression data}}
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\field{title}{{Visualizing denovo RNAseq experiments - Creating a toolchain for storage, visualization and comparison of RNA expression data}}
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\field{year}{2013}
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\endentry
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\endrefsection
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\endinput
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