X-Git-Url: https://git.donarmstrong.com/?p=rsem.git;a=blobdiff_plain;f=WHAT_IS_NEW;h=2c6f2c7c33257c44434857a2359e855e44dd078e;hp=09f4dd9c70d44f7f788ea1abd1b44752b02ba204;hb=0f8fbc39759d8a8a4fa755903b8bde403b0da6c9;hpb=49deb7291ab1a35a319bdc68a4d4d708ec6f011c

diff --git a/WHAT_IS_NEW b/WHAT_IS_NEW
index 09f4dd9..2c6f2c7 100644
--- a/WHAT_IS_NEW
+++ b/WHAT_IS_NEW
@@ -1,3 +1,42 @@
+RSEM v1.2.12
+
+- Enabled allele-specific expression estimation
+- Added '--calc-pme' option for 'rsem-calculate-expression' to calculate posterior mean estimates only (no credibility intervals)
+- Modified the shebang line of RSEM perl scripts to make them more portable
+- Added '--seed' option for 'rsem-simulate-reads' to enable users set the seed of random number generator used by the simulation
+- Modified the transcript extraction behavior of 'rsem-prepare-reference'. For transcripts that cannot be extracted, instead of failing the whole script, warning information is produced. Those transcripts are ignored
+
+--------------------------------------------------------------------------------------------
+
+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