X-Git-Url: https://git.donarmstrong.com/?p=rsem.git;a=blobdiff_plain;f=WHAT_IS_NEW;h=01f9948d2b26dcf11aeb520d084e00c72baf37b3;hp=31025d87755dbf889a055289557f69c1fae75de0;hb=93ebadc957ddade1a7cdcf419b48cbb995ac99bc;hpb=a1dc3c6c442d288c7f4218cbb8b7a54f08e9d980

diff --git a/WHAT_IS_NEW b/WHAT_IS_NEW
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--- a/WHAT_IS_NEW
+++ b/WHAT_IS_NEW
@@ -1,3 +1,63 @@
+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'
+
+--------------------------------------------------------------------------------------------
+
+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
+
+--------------------------------------------------------------------------------------------
+
+RSEM v1.2.6
+
+- Install the latest version of EBSeq from Bioconductor and if fails, try to install EBSeq v1.1.5 locally
+- Fixed a bug in 'rsem-gen-transcript-plots', which makes 'rsem-plot-transcript-wiggles' fail 
+
+--------------------------------------------------------------------------------------------
+
+RSEM v1.2.5
+
+- Updated EBSeq from v1.1.5 to v1.1.6
+- Fixed a bug in 'rsem-generate-data-matrix', which can cause 'rsem-find-DE' to crash 
+
+--------------------------------------------------------------------------------------------
+
+RSEM v1.2.4
+
+- Fixed a bug that leads to poor parallelization performance in Mac OS systems
+- Fixed a problem that may halt the 'rsem-gen-transcript-plots", thanks Han Lin for pointing out the problem and suggesting possible fixes  
+- Added some user-friendly error messages for converting transcript BAM files into genomic BAM files
+- Modified rsem-tbam2gbam so that the original alignment quality MAPQ will be preserved if the input bam is not from RSEM
+- Added user-friendly error messages if users forget to compile the source codes
+
+--------------------------------------------------------------------------------------------
+
+RSEM v1.2.3
+
+- Fixed a bug in 'EBSeq/rsem-for-ebseq-generate-ngvector-from-clustering-info' which may crash the script
+
+--------------------------------------------------------------------------------------------
+
+RSEM v1.2.2
+
+- Updated EBSeq to v1.1.5
+- Modified 'rsem-find-DE' to generate extra output files (type 'rsem-find-DE' to see more information)
+
+--------------------------------------------------------------------------------------------
+
 RSEM v1.2.1
 
 - Added poly(A) tails to 'reference_name.transcripts.fa' so that the RSEM generated transcript unsorted BAM file can be fed into RSEM as an input file. However, users need to rebuild their references if they want to visualize the transcript level wiggle files and BAM files using IGV