X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=WHAT_IS_NEW;h=24ae065d19dc6a56093fba3286d7ff0729a57147;hb=f5dc7f9504136b08210ca8a5f3371060b4c04f60;hp=bf8407a435322afe76abf845d1347a149f506816;hpb=3c03759b005d7ca39d65ddf996d8e440ab5aabb6;p=rsem.git

diff --git a/WHAT_IS_NEW b/WHAT_IS_NEW
index bf8407a..24ae065 100644
--- a/WHAT_IS_NEW
+++ b/WHAT_IS_NEW
@@ -1,7 +1,37 @@
+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
+
+--------------------------------------------------------------------------------------------
+
+RSEM v1.2.9
+
+- Fixed a compilation error problem in Mac OS
+- Fixed a problem in makefile that affects 'make ebseq'
+- Added 'model_file_description.txt', which describes the format and meanings of file 'sample_name.stat/sample_name.model'
+- Updated samtools to version 0.1.19
+
+--------------------------------------------------------------------------------------------
+
+RSEM v1.2.8
+
+- Provided a more detailed description for how to simulate RNA-Seq data using 'rsem-simulate-reads'
+- Provided more user-friendly error message if RSEM fails to extract transcript sequences due to the failure of reading certain chromosome sequences
+
+--------------------------------------------------------------------------------------------
+
 RSEM v1.2.7
 
 - 'rsem-find-DE' is replaced by 'rsem-run-ebseq' and 'rsem-control-fdr' for a more friendly user experience
 - Added support for differential expression testing on more than 2 conditions in RSEM's EBSeq wrappers 'rsem-run-ebseq' and 'rsem-control-fdr'
+- Renamed '--phred33-quals', '--phred64-quals', and '--solexa-quals' in 'rsem-calculate-expression' to '--bowtie-phred33-quals', '--bowtie-phred64-quals', and '--bowtie-solex-quals' to avoid confusion
 
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