Added Bowtie 2 support

[rsem.git] / WHAT_IS_NEW

diff --git a/WHAT_IS_NEW b/WHAT_IS_NEW
index 77f966d1f8fe4b35ab31d40ffda78ccdd941741b..24ae065d19dc6a56093fba3286d7ff0729a57147 100644 (file)
--- a/WHAT_IS_NEW
+++ b/WHAT_IS_NEW
@@ -1,3 +1,10 @@
+RSEM v1.2.11
+
+- Enabled RSEM to use Bowtie 2 aligner (indel, local and discordant alignments are not supported yet)
+- Changed option names '--bowtie-phred33-quals', '--bowtie-phred64-quals' and '--bowtie-solexa-quals' back to '--phred33-quals', '--phred64-quals' and '--solexa-quals' 
+
+--------------------------------------------------------------------------------------------
+
 RSEM v1.2.10
 
 - Fixed a bug which will lead to out-of-memory error when RSEM computes ngvector for EBSeq