rsem v1.1.21

[rsem.git] / WHAT_IS_NEW

diff --git a/WHAT_IS_NEW b/WHAT_IS_NEW
index 2a6cc2f4c14ff8ab19ae00d6a6b8687602adc433..244066c0b5c0617031a2ecd04ae96b1a0437e90f 100644 (file)
--- a/WHAT_IS_NEW
+++ b/WHAT_IS_NEW
@@ -1,3 +1,50 @@
+RSEM v1.1.21
+
+- Removed optional field "Z0:A:!" in the BAM outputs
+- Added --no-fractional-weight option to rsem-bam2wig, if the BAM file is not generated by RSEM, this option is recommended to be set
+- Fixed a bug for generating transcript level wiggle files using 'rsem-plot-transcript-wiggles' 
+
+--------------------------------------------------------------------------------------------
+
+RSEM v1.1.20
+
+- Added an option to set the temporary folder name
+- Removed sample_name.sam.gz. Instead, RSEM uses samtools to convert bowtie outputted SAM file into a BAM file under the temporary folder
+- RSEM generated BAM files now contains all alignment lines produced by bowtie or user-specified aligners, including unalignable reads. Please note that for paired-end reads, if one mate has alignments but the other does not, RSEM will mark the alignable mate as "unmappable" (flag bit 0x4) and append an optional field "Z0:A:!"
+
+--------------------------------------------------------------------------------------------
+
+RSEM v1.1.19
+
+- Allowed > 2^31 hits
+- Added some instructions on how to visualize transcript coordinate BAM/WIG files using IGV
+- Included EBSeq for downstream differential expression analysis
+
+--------------------------------------------------------------------------------------------
+
+RSEM v1.1.18
+
+- Added some user-friendly error messages
+- Added program 'rsem-sam-validator', users can use this program to check if RSEM can process their SAM/BAM files
+- Modified 'convert-sam-for-rsem' so that this program will convert users' SAM/BAM files into acceptable BAM files for RSEM
+
+--------------------------------------------------------------------------------------------
+
+RSEM v1.1.17
+
+- Fixed a bug related to parallezation of credibility intervals calculation
+- Added --no-bam-output option to rsem-calculate-expression
+- The order of @SQ tags in SAM/BAM files can be arbitrary now 
+
+--------------------------------------------------------------------------------------------
+  
+RSEM v1.1.16
+
+- Added --time option to show time consumed by each phase
+- Moved the alignment file out of the temporary folder
+- Enabled pthreads for calculating credibility intervals
+
+--------------------------------------------------------------------------------------------
 
 RSEM v1.1.15
 
@@ -5,6 +52,7 @@ RSEM v1.1.15
 - Modified samtools' Makefile for cygwin. For cygwin users, please uncomment the 4th and 8th lines in sam/Makefile before compiling RSEM
 
 --------------------------------------------------------------------------------------------
+
 RSEM v1.1.14
 
 - Added --chunkmbs option to rsem-calculate-expression (patch contributed by earonesty)