Updated README.md and WHAT_IS_NEW

[rsem.git] / WHAT_IS_NEW

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+RSEM v1.2.14
+
+- 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 
+- 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'
+- 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
+- Added --seed option to set random number generator seeds in 'rsem-calculate-expression'  
+- Added posterior standard deviation of counts as output if either '--calc-pme' or '--calc-ci' is set
+- Updated boost to v1.55.0
+- Renamed makefile as Makefile
+- If '--output-genome-bam' is set, in the genome BAM file, each alignment's 'MD' field will be adjusted to match the CIGAR string
+- '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
+- Added instructions for users who want to put all RSEM executables into a bin directory (see Compilation & Installation section of 'README.md')
+
+--------------------------------------------------------------------------------------------
+
 RSEM v1.2.13
 
 - Allowed users to use the SAMtools in the PATH first and enabled RSEM to find its executables via a symbolic link