diff --git a/public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/templates/pdf/lib_seqeval.tex b/public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/templates/pdf/lib_seqeval.tex index ee2bc6a4fe6bc0e1515599de8d74f870f434b445..472c229449c27bfc517d83fd449636465c9bd5ca 100644 --- a/public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/templates/pdf/lib_seqeval.tex +++ b/public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/templates/pdf/lib_seqeval.tex @@ -99,26 +99,6 @@ More information about clipping using cutadapt is available on the \end{center} \addtocounter{table}{-1} -((* if lib.is_paired_end *)) -After clipping, all read pairs are then checked ('synced') for their -completeness. Read pairs whose other half has been discarded during -clipping, will also be discarded. The summary of this step is available in -Table~\ref{tab:clipsync}. - -\begin{center} - \captionof{table}{Summary of Post-Clipping Sync Step} - \label{tab:clipsync} - \begin{tabular}{ l r } - \hline - Parameter & Count\\ \hline \hline - Discarded FASTQ records from read 1 & ((( lib.flexiprep.stats.fastq_sync.num_reads_discarded_R1|nice_int )))\\ - Discarded FASTQ records from read 2 & ((( lib.flexiprep.stats.fastq_sync.num_reads_discarded_R2|nice_int )))\\ - \hline - Total kept FASTQ records & ((( lib.flexiprep.stats.fastq_sync.num_reads_kept|nice_int )))\\ - \hline - \end{tabular} -\end{center} -((* endif *)) ((* endif *)) \vspace{2mm} @@ -141,8 +121,8 @@ Table~\ref{tab:clipsync}. \begin{tabular}{ l r } \hline Parameter & Count\\ \hline \hline - Discarded FASTQ records from read 1 & ((( lib.flexiprep.stats.trimming_R1.num_reads_discarded|nice_int )))\\ - Discarded FASTQ records from read 2 & ((( lib.flexiprep.stats.trimming_R2.num_reads_discarded|nice_int )))\\ + Discarded FASTQ records from read 1 & ((( lib.flexiprep.stats.trimming_R1.num_reads_discarded_total|nice_int )))\\ + Discarded FASTQ records from read 2 & ((( lib.flexiprep.stats.trimming_R2.num_reads_discarded_total|nice_int )))\\ \hline \end{tabular} \end{center}