Added Bowtie 2 support

[rsem.git] / README.md

diff --git a/README.md b/README.md
index 725d1cb9c0cc1481a0c0725ee327508d27c6565c..f6a88dc2b41a7ed1a3f8fd56561114cec7bcb35c 100644 (file)
--- a/README.md
+++ b/README.md
@@ -60,8 +60,10 @@ variable.
 
 C++, Perl and R are required to be installed. 
 
-To take advantage of RSEM's built-in support for the Bowtie alignment
-program, you must have [Bowtie](http://bowtie-bio.sourceforge.net) installed.
+To take advantage of RSEM's built-in support for the Bowtie/Bowtie 2
+alignment program, you must have
+[Bowtie](http://bowtie-bio.sourceforge.net) and/or [Bowtie
+2](http://bowtie-bio.sourceforge.net/bowtie2) installed.
 
 ## <a name="usage"></a> Usage
 
@@ -107,7 +109,13 @@ consideration.
 #### Using an alternative aligner
 
 By default, RSEM automates the alignment of reads to reference
-transcripts using the Bowtie alignment program.  To use an alternative
+transcripts using the Bowtie alignment program. Turn on '--bowtie2'
+for 'rsem-prepare-reference' and 'rsem-calculate-expression' will
+allow RSEM to use the Bowtie 2 alignment program instead. Please note
+that indel alignments, local alignments and discordant alignments are
+disallowed when RSEM uses Bowtie 2 since RSEM currently cannot handle
+them. See the description of '--bowtie2' option in
+'rsem-calculate-expression' for more details. To use an alternative
 alignment program, align the input reads against the file
 'reference_name.idx.fa' generated by 'rsem-prepare-reference', and
 format the alignment output in SAM or BAM format.  Then, instead of
@@ -437,7 +445,7 @@ be sent to <a href="mailto:nleng@wisc.edu">Ning Leng</a>.
 
 ## <a name="authors"></a> Authors
 
-RSEM is developed by Bo Li, with substaintial technical input from Colin Dewey.
+The RSEM algorithm is developed by Bo Li and Colin Dewey. The RSEM software is mainly implemented by Bo Li.
 
 ## <a name="acknowledgements"></a> Acknowledgements