Added user-friendly error messages if users forget to compile the source codes

[rsem.git] / WHAT_IS_NEW

diff --git a/WHAT_IS_NEW b/WHAT_IS_NEW
index ddcfd959f2accbb06da8a57ef93208aff7a1264d..64dc6e55768b12dc467e1909b84a964c7dab3d9a 100644 (file)
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+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
+- Modified 'rsem-tbam2gbam' to convert users' alignments from transcript BAM files into genome BAM files, provided users use 'reference_name.idx.fa' to build indices for their aligners
+- Updated EBSeq from v1.1.3 to v1.1.4
+- Corrected several typos in warning messages
+
+--------------------------------------------------------------------------------------------
+
+RSEM v1.2.0
+
+- Changed output formats, added FPKM field etc.
+- Fixed a bug related to paired-end reads data
+- Added a script to run EBSeq automatically and updated EBSeq to v1.1.3
+
+--------------------------------------------------------------------------------------------
+
+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