From: Bo Li Date: Mon, 16 Jun 2014 08:25:37 +0000 (-0500) Subject: Updated WHAT_IS_NEW X-Git-Url: https://git.donarmstrong.com/?p=rsem.git;a=commitdiff_plain;h=83ce658a4b9c5f04c081316314b66b94ad5ffbde Updated WHAT_IS_NEW --- diff --git a/WHAT_IS_NEW b/WHAT_IS_NEW index f698418..08c743d 100644 --- a/WHAT_IS_NEW +++ b/WHAT_IS_NEW @@ -1,3 +1,12 @@ +RSEM v1.2.15 + +- Allowed for a subset of reference sequences to be declared in an input SAM/BAM file +- For any transcript not declared in the SAM/BAM file, its PME estimates and credibility intervals are set to zero +- Added advanced options for customizing Gibbs sampler and credibility interval calculation behaviors +- Splitted options in 'rsem-calculate-expression' into basic and advanced options; + +-------------------------------------------------------------------------------------------- + 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