3 - Allowed users to use the SAMtools in the PATH first and enabled RSEM to find its executables via a symbolic link
4 - Changed the behavior of parsing GTF file. Now if a GTF line's feature is not "exon" and it does not contain a "gene_id" or "transcript_id" attribute, only a warning message will be produced (instead of failing the RSEM)
6 --------------------------------------------------------------------------------------------
10 - Enabled allele-specific expression estimation
11 - Added '--calc-pme' option for 'rsem-calculate-expression' to calculate posterior mean estimates only (no credibility intervals)
12 - Modified the shebang line of RSEM perl scripts to make them more portable
13 - Added '--seed' option for 'rsem-simulate-reads' to enable users set the seed of random number generator used by the simulation
14 - 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
16 --------------------------------------------------------------------------------------------
20 - Enabled RSEM to use Bowtie 2 aligner (indel, local and discordant alignments are not supported yet)
21 - Changed option names '--bowtie-phred33-quals', '--bowtie-phred64-quals' and '--bowtie-solexa-quals' back to '--phred33-quals', '--phred64-quals' and '--solexa-quals'
23 --------------------------------------------------------------------------------------------
27 - Fixed a bug which will lead to out-of-memory error when RSEM computes ngvector for EBSeq
29 --------------------------------------------------------------------------------------------
33 - Fixed a compilation error problem in Mac OS
34 - Fixed a problem in makefile that affects 'make ebseq'
35 - Added 'model_file_description.txt', which describes the format and meanings of file 'sample_name.stat/sample_name.model'
36 - Updated samtools to version 0.1.19
38 --------------------------------------------------------------------------------------------
42 - Provided a more detailed description for how to simulate RNA-Seq data using 'rsem-simulate-reads'
43 - Provided more user-friendly error message if RSEM fails to extract transcript sequences due to the failure of reading certain chromosome sequences
45 --------------------------------------------------------------------------------------------
49 - 'rsem-find-DE' is replaced by 'rsem-run-ebseq' and 'rsem-control-fdr' for a more friendly user experience
50 - Added support for differential expression testing on more than 2 conditions in RSEM's EBSeq wrappers 'rsem-run-ebseq' and 'rsem-control-fdr'
51 - 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
53 --------------------------------------------------------------------------------------------
57 - Install the latest version of EBSeq from Bioconductor and if fails, try to install EBSeq v1.1.5 locally
58 - Fixed a bug in 'rsem-gen-transcript-plots', which makes 'rsem-plot-transcript-wiggles' fail
60 --------------------------------------------------------------------------------------------
64 - Updated EBSeq from v1.1.5 to v1.1.6
65 - Fixed a bug in 'rsem-generate-data-matrix', which can cause 'rsem-find-DE' to crash
67 --------------------------------------------------------------------------------------------
71 - Fixed a bug that leads to poor parallelization performance in Mac OS systems
72 - Fixed a problem that may halt the 'rsem-gen-transcript-plots", thanks Han Lin for pointing out the problem and suggesting possible fixes
73 - Added some user-friendly error messages for converting transcript BAM files into genomic BAM files
74 - Modified rsem-tbam2gbam so that the original alignment quality MAPQ will be preserved if the input bam is not from RSEM
75 - Added user-friendly error messages if users forget to compile the source codes
77 --------------------------------------------------------------------------------------------
81 - Fixed a bug in 'EBSeq/rsem-for-ebseq-generate-ngvector-from-clustering-info' which may crash the script
83 --------------------------------------------------------------------------------------------
87 - Updated EBSeq to v1.1.5
88 - Modified 'rsem-find-DE' to generate extra output files (type 'rsem-find-DE' to see more information)
90 --------------------------------------------------------------------------------------------
94 - 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
95 - 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
96 - Updated EBSeq from v1.1.3 to v1.1.4
97 - Corrected several typos in warning messages
99 --------------------------------------------------------------------------------------------
103 - Changed output formats, added FPKM field etc.
104 - Fixed a bug related to paired-end reads data
105 - Added a script to run EBSeq automatically and updated EBSeq to v1.1.3
107 --------------------------------------------------------------------------------------------
111 - Removed optional field "Z0:A:!" in the BAM outputs
112 - Added --no-fractional-weight option to rsem-bam2wig, if the BAM file is not generated by RSEM, this option is recommended to be set
113 - Fixed a bug for generating transcript level wiggle files using 'rsem-plot-transcript-wiggles'
115 --------------------------------------------------------------------------------------------
119 - Added an option to set the temporary folder name
120 - Removed sample_name.sam.gz. Instead, RSEM uses samtools to convert bowtie outputted SAM file into a BAM file under the temporary folder
121 - 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:!"
123 --------------------------------------------------------------------------------------------
127 - Allowed > 2^31 hits
128 - Added some instructions on how to visualize transcript coordinate BAM/WIG files using IGV
129 - Included EBSeq for downstream differential expression analysis
131 --------------------------------------------------------------------------------------------
135 - Added some user-friendly error messages
136 - Added program 'rsem-sam-validator', users can use this program to check if RSEM can process their SAM/BAM files
137 - Modified 'convert-sam-for-rsem' so that this program will convert users' SAM/BAM files into acceptable BAM files for RSEM
139 --------------------------------------------------------------------------------------------
143 - Fixed a bug related to parallezation of credibility intervals calculation
144 - Added --no-bam-output option to rsem-calculate-expression
145 - The order of @SQ tags in SAM/BAM files can be arbitrary now
147 --------------------------------------------------------------------------------------------
151 - Added --time option to show time consumed by each phase
152 - Moved the alignment file out of the temporary folder
153 - Enabled pthreads for calculating credibility intervals
155 --------------------------------------------------------------------------------------------
159 - Fixed several bugs causing compilation error
160 - Modified samtools' Makefile for cygwin. For cygwin users, please uncomment the 4th and 8th lines in sam/Makefile before compiling RSEM
162 --------------------------------------------------------------------------------------------
166 - Added --chunkmbs option to rsem-calculate-expression (patch contributed by earonesty)
167 - Added --sampling-for-bam option to rsem-calculate-expression, in the bam file, instead of providing expected weights, for each read RSEM samples one alignment based on the expected weights
168 - RSEM can generate BAM and Wiggle files in both genomic-coordinate and transcript-coordinate
169 - Added rsem-plot-transcript-wiggles. This script can generate transcript-coordinate wiggle plots in pdf format. One unique feature is, a stacked plot can be generated, with unique read contribution shown as black and multi-read contribution shown as red
170 - Added convert_sam_for_rsem script for users do not use bowtie aligner
171 - Modified RSEM's GTF file parser. Now RSEM does not require "transcript_id" and "gene_id" be the first two attributes shown
172 - Improved descriptions for thread related errors