X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=README.md;fp=README.md;h=f6a88dc2b41a7ed1a3f8fd56561114cec7bcb35c;hb=66a1547e5d549a915cefb729222be915b87fb34d;hp=725d1cb9c0cc1481a0c0725ee327508d27c6565c;hpb=cee60cca5d914c7e6e880cb8276cdb5b129458c7;p=rsem.git
diff --git a/README.md b/README.md
index 725d1cb..f6a88dc 100644
--- 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.
## 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 Ning Leng.
## 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.
## Acknowledgements