Changed year to 2024.

Author: V-Z

README.md

@@ -1,8 +1,8 @@
-# HybSeq course 2023
+# HybSeq course 2024
 
 Course to learn all theory about HybSeq and practically learn how to analyze HybSeq data, how to solve all problems, and how to evaluate differences among gene trees. Important part is enough time to discuss everything, including practical problems and projects of individual participants.
 
-* Information about the course: <https://trapa.cz/en/hybseq-course-2023>
+* Information about the course: <https://trapa.cz/en/hybseq-course-2024>
 * Contact author: <https://trapa.cz/en/contact>
 
 ## License

presentation/hybseq_course.tex

@@ -625,7 +625,7 @@ \subsection{Processing input files}
 		\item Script \texttt{$\sim$/hybseq/bin/hybseq\_2\_hybpiper\_1\_submitter.sh} goes to directory set by \texttt{DATADIR} variable and for every sample (pair of forward and reverse FASTQ files) listed in \texttt{samples\_list.txt} (variable \texttt{SAMPLES}, created by \texttt{hybseq\_1\_prep\_2\_run.sh}) and submits via \texttt{qsub} individual task for each input sample (thy are processed independently in parallel)
 		\item Script \texttt{$\sim$/hybseq/bin/hybseq\_run\_2\_hybpiper\_2\_qsub.sh} drives submission and manipulation of processing of each individual file --- it checks if all required data are provided, copy input files to \texttt{SCRATCHDIR}, loads required software modules, runs processing itself by \texttt{hybseq\_2\_hybpiper\_3\_run.sh} and copy results back
 		\item Script \texttt{$\sim$/hybseq/bin/hybseq\_2\_hybpiper\_3\_run.sh} runs all HybPiper steps for individual samples (as submitted by previous scripts)
-		\item Outputs of \texttt{$\sim$/hybseq/bin/hybseq\_2\_hybpiper\_3\_run.sh} should be checked and moved into special directory (\texttt{$\sim$/hybseq\_course\_2023\_zingibers/2\_seqs}) where new list of samples must be created
+		\item Outputs of \texttt{$\sim$/hybseq/bin/hybseq\_2\_hybpiper\_3\_run.sh} should be checked and moved into special directory (\texttt{$\sim$/hybseq\_course\_zingibers/2\_seqs}) where new list of samples must be created
 		\item Script \texttt{$\sim$/hybseq/bin/hybseq\_run\_3\_hybpiper\_postprocess\_1\_qsub.sh} can be then used to run \texttt{$\sim$/hybseq/bin/hybseq\_3\_hybpiper\_postprocess\_2\_run.sh} which uses HybPiper to retrieve sequences of exons, introns and supercontigs; prints statistics, creates heatmaps, and summaries paralogs warnings --- retrieved sequences can then be aligned (see further)
 	\end{itemize}
 \end{frame}