Updated manual.

CHANGES.md

@@ -1,5 +1,5 @@
 * Fixed a bug in --quantMode TranscriptomeSAM that prevented output to Aligned.toTranscriptome.out.bam of the reads mapped to the very last annotated transcript.
-* Cleaned up the code to remove compilation warnings.
+* Cleaned up the code to remove compilation warnings (thanks to github.com/yhoogstrate).
 * Implemented --outSAMunmapped Within KeepPairs option to record unmapped mate adjacent to the mapped one, in case single-end alignments are allowed.
   For multi-mappers, the unmapped mate will be recored mulitple times adjacent to the mappet mate of each alignment.
 

extras/doc-latex/STARmanual.tex

@@ -34,8 +34,8 @@
 
 \newcommand{\sechyperref}[1]{\hyperref[#1]{Section \ref{#1}. \nameref{#1}}}
 
-\title{STAR manual 2.5.0a}
-\author{Alexnder Dobin\\
+\title{STAR manual 2.5.1a}
+\author{Alexander Dobin\\
 [email protected]}
 \maketitle
 \tableofcontents
@@ -150,7 +150,7 @@ \subsubsection{Using a list of annotated junctions.}
 Note, that the \opt{sjdbFileChrStartEnd} file can contain duplicate (identical) junctions, STAR will collapse (remove) duplicate junctions.
 
 \subsubsection{Very small genome.}
-For small genomes, the parameter \opt{genomeSAindexNbases} needs to be scaled down, with a typical value of \code{min(14, log2(GenomeLength)/2 - 1)}. For example, for 1~megaBase genome, this is equal to 9, for 100~kiloBase genome, this is equal to 7.
+For small genomes, the parameter \opt{genomeSAindexNbases} \textbf{must} to be scaled down, with a typical value of \code{min(14, log2(GenomeLength)/2 - 1)}. For example, for 1~megaBase genome, this is equal to 9, for 100~kiloBase genome, this is equal to 7.
 
 \subsubsection{Genome with a large number of references.}
 If you are using a genome with a large (\textgreater 5,000) number of references (chrosomes/scaffolds), you may need to reduce the \opt{genomeChrBinNbits} to reduce RAM consumption. The following scaling is recommended: \opt{genomeChrBinNbits} = \code{min(18, log2(GenomeLength/NumberOfReferences))}. For example, for 3~gigaBase genome with 100,000 chromosomes/scaffolds, this is equal to 15.
@@ -303,8 +303,9 @@ \subsection{Splice junctions.}
 
 \section{Chimeric and circular alignments.}
 To switch on detection of chimeric (fusion) alignments (in addition to normal mapping), \opt{chimSegmentMin} should be set to a positive value. Each chimeric alignment consists of two "segments". Each segment is non-chimeric on its own, but the segments are chimeric to each other (i.e. the segments belong to different chromosomes, or different strands, or are far from each other). Both segments may contain splice junctions, and one of the segments may contain portions of both mates. \opt{chimSegmentMin} parameter controls the minimum mapped length of the two segments that is allowed. For example, if you have 2x75 reads and used \opt{chimSegmentMin} 20, a chimeric alignment with 130b on one chromosome and 20b on the other will be output, while 135 + 15 won't be.
+
 \subsection{STAR-Fusion.}
-STAR-Fusion is a software package for detecting fusion transcript from STAR chimeric output. It is developed and maintained by Brian Haas. Please visit its GitHub page for instructions and documentation: \url{https://github.com/STAR-Fusion/STAR-Fusion}.
+STAR-Fusion is a software package for detecting fusion transcript from STAR chimeric output. It is developed and maintained by Brian Haas (@Broad Institute), whose effort was  inspired by earlier work done by Nicolas Stransky in the landmark publication "The landscape of kinase fusions in cancer" by Stransky et al., Nat Commun 2014, in addition to very nice work done by Daniel Nicorici with his FusionCatcher software. Please visit its GitHub page for instructions and documentation: \url{https://github.com/STAR-Fusion/STAR-Fusion}.
 
 \subsection{Chimeric alignments in the main BAM files.}
 Chimeric alignments can be included together with normal alignments in the main (sorted or unsorted) BAM file(s) using \opt{chimOutType} \optv{WithinBAM}. In these files, formatting of chimeric alignments follows the latest SAM/BAM specifications.

extras/doc-latex/parametersDefault.tex

@@ -67,6 +67,9 @@
 \optName{genomeSAsparseD}
   \optValue{1}
   \optLine{int{\textgreater}0: suffux array sparsity, i.e. distance between indices: use bigger numbers to decrease needed RAM at the cost of mapping speed reduction} 
+\optName{genomeSuffixLengthMax}
+  \optValue{-1}
+  \optLine{int: maximum length of the suffixes, has to be longer than read length. -1 = infinite.} 
 \end{optTable}
 \optSection{Splice Junctions Database}\label{Splice_Junctions_Database}
 \begin{optTable}
@@ -188,7 +191,7 @@
 \end{optOptTable}
 \optName{outReadsUnmapped}
   \optValue{None}
-  \optLine{string: output of unmapped reads (besides SAM)} 
+  \optLine{string: output of unmapped and partially mapped (i.e. mapped only one mate of a paired end read) reads in separate file(s).} 
 \begin{optOptTable}
   \optOpt{None}   \optOptLine{no output}
   \optOpt{Fastx}   \optOptLine{output in separate fasta/fastq files, Unmapped.out.mate1/2}
@@ -249,11 +252,17 @@
   \optLine{int{\textgreater}=0:                     start value for the IH attribute. 0 may be required by some downstream software, such as Cufflinks or StringTie.} 
 \optName{outSAMunmapped}
   \optValue{None}
-  \optLine{string: output of unmapped reads in the SAM format} 
+  \optLine{string(s): output of unmapped reads in the SAM format} 
+  \optLine{1st word:} 
 \begin{optOptTable}
   \optOpt{None}   \optOptLine{no output}
   \optOpt{Within}   \optOptLine{output unmapped reads within the main SAM file (i.e. Aligned.out.sam)}
 \end{optOptTable}
+  \optLine{2nd word:} 
+\begin{optOptTable}
+  \optOpt{KeepPairs}   \optOptLine{record unmapped mate for each alignment, and, in case of unsroted output, keep it adjacent to its mapped mate.}
+\end{optOptTable}
+  \optLine{Only affects multi-mapping reads} 
 \optName{outSAMorder}
   \optValue{Paired}
   \optLine{string: type of sorting for the SAM output} 
@@ -377,28 +386,29 @@
   \optLine{int: the score range below the maximum score for multimapping alignments} 
 \optName{outFilterMultimapNmax}
   \optValue{10}
-  \optLine{int: read alignments will be output only if the read maps fewer than this value, otherwise no alignments will be output} 
+  \optLine{int: maximum number of loci the read is allowed to map to. Alignments (all of them) will be output only if the read maps to no more loci than this value. } 
+  \optLine{Otherwise no alignments will be output, and the read will be counted as "mapped to too many loci" in the Log.final.out .} 
 \optName{outFilterMismatchNmax}
   \optValue{10}
-  \optLine{int: alignment will be output only if it has fewer mismatches than this value} 
+  \optLine{int: alignment will be output only if it has no more mismatches than this value.} 
 \optName{outFilterMismatchNoverLmax}
   \optValue{0.3}
-  \optLine{int: alignment will be output only if its ratio of mismatches to *mapped* length is less than this value} 
+  \optLine{float: alignment will be output only if its ratio of mismatches to *mapped* length is less than or equal to this value.} 
 \optName{outFilterMismatchNoverReadLmax}
-  \optValue{1}
-  \optLine{int: alignment will be output only if its ratio of mismatches to *read* length is less than this value} 
+  \optValue{1.0}
+  \optLine{float: alignment will be output only if its ratio of mismatches to *read* length is less than or equal to this value.} 
 \optName{outFilterScoreMin}
   \optValue{0}
-  \optLine{int: alignment will be output only if its score is higher than this value} 
+  \optLine{int: alignment will be output only if its score is higher than or equal to this value.} 
 \optName{outFilterScoreMinOverLread}
   \optValue{0.66}
-  \optLine{float: outFilterScoreMin normalized to read length (sum of mates' lengths for paired-end reads)} 
+  \optLine{float: same as outFilterScoreMin, but  normalized to read length (sum of mates' lengths for paired-end reads)} 
 \optName{outFilterMatchNmin}
   \optValue{0}
-  \optLine{int: alignment will be output only if the number of matched bases is higher than this value} 
+  \optLine{int: alignment will be output only if the number of matched bases is higher than or equal to this value.} 
 \optName{outFilterMatchNminOverLread}
   \optValue{0.66}
-  \optLine{float: outFilterMatchNmin normalized to read length (sum of mates' lengths for paired-end reads)} 
+  \optLine{float: sam as outFilterMatchNmin, but normalized to the read length (sum of mates' lengths for paired-end reads).} 
 \optName{outFilterIntronMotifs}
   \optValue{None}
   \optLine{string: filter alignment using their motifs}