X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=README.md;h=4184f5d44caf4d94ebb8c5445f25d531517931d8;hb=799735d94b6f8c5c34b828bccdd3408f4b38a6ef;hp=9fe0297fd769b705ba0bf1969046c73d47f869af;hpb=c729fa33c6e2f9e3e1b374c66a55265525e7d974;p=rsem.git diff --git a/README.md b/README.md index 9fe0297..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 @@ -457,9 +462,9 @@ RSEM uses the [Boost C++](http://www.boost.org) and [EBSeq](http://www.biostat.wisc.edu/~ningleng/EBSeq_Package/) for differential expression analysis. -We thank earonesty, Dr. Samuel Arvidsson for contributing patches. +We thank earonesty and Dr. Samuel Arvidsson for contributing patches. -We thank Han Lin, j.miller for suggesting possible fixes. +We thank Han Lin, j.miller, Joël Fillon, Dr. Samuel G. Younkin and Malcolm Cook for suggesting possible fixes. ## License