Updated manual - highlightet need of removal of plastid sequences

manual/sondovac_manual.tex

@@ -848,8 +848,8 @@ \subsection{Input and output files}
   \item \texttt{*$\_$prelim$\_$probe$\_$seq$\_$cluster$\_$90.clstr} -- Unclustered exons and clustered exons with more than a certain sequence similarity (CLSTR file).
   \item \texttt{*$\_$unique$\_$prelim$\_$probe$\_$seq.fasta} -- Unclustered exons / exons with less than a certain sequence similarity.
   \item \texttt{*$\_$similarity$\_$test.fasta} -- Contigs that comprise exons $\geq$ bait length and have a~certain total locus length.
-  \item \texttt{*$\_$target$\_$enrichment$\_$probe$\_$sequences.fasta} -- \textbf{Final probes in FASTA.}
-  \item \texttt{*$\_$possible$\_$cp$\_$dna$\_$gene$\_$in$\_$probe$\_$set.pslx} -- In case of any BLAT hits, the user needs to manually remove these plastid probe sequences from \texttt{*$\_$target$\_$enrichment$\_$probe$\_$se\-quences.fasta}; the remaining ones are the final probe sequences in FASTA.
+  \item \underline{\texttt{*$\_$target$\_$enrichment$\_$probe$\_$sequences.fasta} -- \textbf{Final probes in FASTA.}}
+  \item \texttt{*$\_$possible$\_$cp$\_$dna$\_$gene$\_$in$\_$probe$\_$set.pslx} -- \hl{\textbf{In case of any BLAT hits, the user needs to manually remove these plastid probe sequences}} from \texttt{*$\_$target$\_$enrichm\-ent$\_$probe$\_$sequences.fasta}; the remaining ones are the final probe sequences in FASTA. \hl{\textbf{Not removing them will take lots of space on the Illumina lane for enriched plastid reads that should actually be available for enriched nuclear reads.}}
 \end{enumerate}
 
 An asterisk (*) denotes the beginning of the output files' names specified by the user with parameter \texttt{-o}. If the user does not select a~custom name, the default value (\texttt{output}) will be used. By default, output files are created in the same directory from which Sondovač was launched. Output files can be saved in a~custom directory by specifying an output directory with parameter \texttt{-o}: