3 - Added error detection for cases such as a read's two mates having different names or a read is both alignable and unalignable
5 --------------------------------------------------------------------------------------------
9 - Corrected a typo in 'rsem-generate-data-matrix', this script extracts 'expected_count' column instead of 'TPM' column
11 --------------------------------------------------------------------------------------------
15 - Allowed for a subset of reference sequences to be declared in an input SAM/BAM file
16 - For any transcript not declared in the SAM/BAM file, its PME estimates and credibility intervals are set to zero
17 - Added advanced options for customizing Gibbs sampler and credibility interval calculation behaviors
18 - Splitted options in 'rsem-calculate-expression' into basic and advanced options
20 --------------------------------------------------------------------------------------------
24 - Changed RSEM's behaviors for building Bowtie/Bowtie 2 indices. In 'rsem-prepare-reference', '--no-bowtie' and '--no-ntog' options are removed. By default, RSEM does not build either Bowtie or Bowtie 2 indices. Instead, it generates two index Multi-FASTA files, 'reference_name.idx.fa' and 'reference_name.n2g.idx.fa'. Compared to the former file, the latter one in addition converts all 'N's into 'G's. These two files can be used to build aligner indices for customized aligners. In addition, 'reference_name.transcripts.fa' does not have poly(A) tails added. To enable RSEM build Bowtie/Bowtie 2 indices, '--bowtie' or '--bowtie2' must be set explicitly. The most significant benefit of this change is that now we can build Bowtie and Bowtie 2 indices simultaneously by turning both '--bowtie' and '--bowtie2' on. Type 'rsem-prepare-reference --help' for more information
25 - If transcript coordinate files are visualized using IGV, 'reference_name.idx.fa' should be imported as a genome (instead of 'reference_name.transcripts.fa'). For more information, see the third subsection of Visualization in 'README.md'
26 - Modified RSEM perl scripts so that RSEM directory will be added in the beginning of the PATH variable. This also means RSEM will try to use its own samtools first
27 - Added --seed option to set random number generator seeds in 'rsem-calculate-expression'
28 - Added posterior standard deviation of counts as output if either '--calc-pme' or '--calc-ci' is set
29 - Updated boost to v1.55.0
30 - Renamed makefile as Makefile
31 - If '--output-genome-bam' is set, in the genome BAM file, each alignment's 'MD' field will be adjusted to match the CIGAR string
32 - 'XS:A:value' field is required by Cufflinks for spliced alignments. If '--output-genome-bam' is set, in the genome BAM file, first each alignment's 'XS' filed will be deleted. Then if the alignment is an spliced alignment, a 'XS:A:value' field will be added accordingly
33 - Added instructions for users who want to put all RSEM executables into a bin directory (see Compilation & Installation section of 'README.md')
35 --------------------------------------------------------------------------------------------
39 - Allowed users to use the SAMtools in the PATH first and enabled RSEM to find its executables via a symbolic link
40 - 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)
42 --------------------------------------------------------------------------------------------
46 - Enabled allele-specific expression estimation
47 - Added '--calc-pme' option for 'rsem-calculate-expression' to calculate posterior mean estimates only (no credibility intervals)
48 - Modified the shebang line of RSEM perl scripts to make them more portable
49 - Added '--seed' option for 'rsem-simulate-reads' to enable users set the seed of random number generator used by the simulation
50 - 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
52 --------------------------------------------------------------------------------------------
56 - Enabled RSEM to use Bowtie 2 aligner (indel, local and discordant alignments are not supported yet)
57 - Changed option names '--bowtie-phred33-quals', '--bowtie-phred64-quals' and '--bowtie-solexa-quals' back to '--phred33-quals', '--phred64-quals' and '--solexa-quals'
59 --------------------------------------------------------------------------------------------
63 - Fixed a bug which will lead to out-of-memory error when RSEM computes ngvector for EBSeq
65 --------------------------------------------------------------------------------------------
69 - Fixed a compilation error problem in Mac OS
70 - Fixed a problem in makefile that affects 'make ebseq'
71 - Added 'model_file_description.txt', which describes the format and meanings of file 'sample_name.stat/sample_name.model'
72 - Updated samtools to version 0.1.19
74 --------------------------------------------------------------------------------------------
78 - Provided a more detailed description for how to simulate RNA-Seq data using 'rsem-simulate-reads'
79 - Provided more user-friendly error message if RSEM fails to extract transcript sequences due to the failure of reading certain chromosome sequences
81 --------------------------------------------------------------------------------------------
85 - 'rsem-find-DE' is replaced by 'rsem-run-ebseq' and 'rsem-control-fdr' for a more friendly user experience
86 - Added support for differential expression testing on more than 2 conditions in RSEM's EBSeq wrappers 'rsem-run-ebseq' and 'rsem-control-fdr'
87 - 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
89 --------------------------------------------------------------------------------------------
93 - Install the latest version of EBSeq from Bioconductor and if fails, try to install EBSeq v1.1.5 locally
94 - Fixed a bug in 'rsem-gen-transcript-plots', which makes 'rsem-plot-transcript-wiggles' fail
96 --------------------------------------------------------------------------------------------
100 - Updated EBSeq from v1.1.5 to v1.1.6
101 - Fixed a bug in 'rsem-generate-data-matrix', which can cause 'rsem-find-DE' to crash
103 --------------------------------------------------------------------------------------------
107 - Fixed a bug that leads to poor parallelization performance in Mac OS systems
108 - Fixed a problem that may halt the 'rsem-gen-transcript-plots", thanks Han Lin for pointing out the problem and suggesting possible fixes
109 - Added some user-friendly error messages for converting transcript BAM files into genomic BAM files
110 - Modified rsem-tbam2gbam so that the original alignment quality MAPQ will be preserved if the input bam is not from RSEM
111 - Added user-friendly error messages if users forget to compile the source codes
113 --------------------------------------------------------------------------------------------
117 - Fixed a bug in 'EBSeq/rsem-for-ebseq-generate-ngvector-from-clustering-info' which may crash the script
119 --------------------------------------------------------------------------------------------
123 - Updated EBSeq to v1.1.5
124 - Modified 'rsem-find-DE' to generate extra output files (type 'rsem-find-DE' to see more information)
126 --------------------------------------------------------------------------------------------
130 - 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
131 - 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
132 - Updated EBSeq from v1.1.3 to v1.1.4
133 - Corrected several typos in warning messages
135 --------------------------------------------------------------------------------------------
139 - Changed output formats, added FPKM field etc.
140 - Fixed a bug related to paired-end reads data
141 - Added a script to run EBSeq automatically and updated EBSeq to v1.1.3
143 --------------------------------------------------------------------------------------------
147 - Removed optional field "Z0:A:!" in the BAM outputs
148 - Added --no-fractional-weight option to rsem-bam2wig, if the BAM file is not generated by RSEM, this option is recommended to be set
149 - Fixed a bug for generating transcript level wiggle files using 'rsem-plot-transcript-wiggles'
151 --------------------------------------------------------------------------------------------
155 - Added an option to set the temporary folder name
156 - Removed sample_name.sam.gz. Instead, RSEM uses samtools to convert bowtie outputted SAM file into a BAM file under the temporary folder
157 - 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:!"
159 --------------------------------------------------------------------------------------------
163 - Allowed > 2^31 hits
164 - Added some instructions on how to visualize transcript coordinate BAM/WIG files using IGV
165 - Included EBSeq for downstream differential expression analysis
167 --------------------------------------------------------------------------------------------
171 - Added some user-friendly error messages
172 - Added program 'rsem-sam-validator', users can use this program to check if RSEM can process their SAM/BAM files
173 - Modified 'convert-sam-for-rsem' so that this program will convert users' SAM/BAM files into acceptable BAM files for RSEM
175 --------------------------------------------------------------------------------------------
179 - Fixed a bug related to parallezation of credibility intervals calculation
180 - Added --no-bam-output option to rsem-calculate-expression
181 - The order of @SQ tags in SAM/BAM files can be arbitrary now
183 --------------------------------------------------------------------------------------------
187 - Added --time option to show time consumed by each phase
188 - Moved the alignment file out of the temporary folder
189 - Enabled pthreads for calculating credibility intervals
191 --------------------------------------------------------------------------------------------
195 - Fixed several bugs causing compilation error
196 - Modified samtools' Makefile for cygwin. For cygwin users, please uncomment the 4th and 8th lines in sam/Makefile before compiling RSEM
198 --------------------------------------------------------------------------------------------
202 - Added --chunkmbs option to rsem-calculate-expression (patch contributed by earonesty)
203 - 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
204 - RSEM can generate BAM and Wiggle files in both genomic-coordinate and transcript-coordinate
205 - 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
206 - Added convert_sam_for_rsem script for users do not use bowtie aligner
207 - Modified RSEM's GTF file parser. Now RSEM does not require "transcript_id" and "gene_id" be the first two attributes shown
208 - Improved descriptions for thread related errors