From b64d62d49f9b0446f10f87a2aadcde2f36854ab6 Mon Sep 17 00:00:00 2001 From: Bo Li Date: Sun, 8 Jun 2014 23:48:03 -0500 Subject: [PATCH] Updated README.md and WHAT_IS_NEW --- README.md | 7 ++++++- WHAT_IS_NEW | 15 +++++++++++++++ 2 files changed, 21 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 902e806..4184f5d 100644 --- a/README.md +++ b/README.md @@ -56,6 +56,11 @@ To compile EBSeq, which is included in the RSEM package, run To install, simply put the rsem directory in your environment's PATH variable. +If you prefer to put all RSEM executables to a bin directory, please +also remember to put 'rsem_perl_utils.pm' and 'WHAT_IS_NEW' to the +same bin directory. 'rsem_perl_utils.pm' is required for most RSEM's +perl scripts and 'WHAT_IS_NEW' contains the RSEM version information. + ### Prerequisites C++, Perl and R are required to be installed. @@ -209,7 +214,7 @@ Here are some guidance for visualizing transcript coordinate files using IGV: 1) Import the transcript sequences as a genome -Select File -> Import Genome, then fill in ID, Name and Fasta file. Fasta file should be 'reference_name.transcripts.fa'. After that, click Save button. Suppose ID is filled as 'reference_name', a file called 'reference_name.genome' will be generated. Next time, we can use: File -> Load Genome, then select 'reference_name.genome'. +Select File -> Import Genome, then fill in ID, Name and Fasta file. Fasta file should be 'reference_name.idx.fa'. After that, click Save button. Suppose ID is filled as 'reference_name', a file called 'reference_name.genome' will be generated. Next time, we can use: File -> Load Genome, then select 'reference_name.genome'. 2) Load visualization files diff --git a/WHAT_IS_NEW b/WHAT_IS_NEW index ecd93cf..f698418 100644 --- a/WHAT_IS_NEW +++ b/WHAT_IS_NEW @@ -1,3 +1,18 @@ +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 -- 2.39.2