X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=README.md;h=b93678dd78421a6c1bf1bfe571c7621683f29cfd;hb=f5dc7f9504136b08210ca8a5f3371060b4c04f60;hp=5c6943bd42f32d5631228267cd19aa1cffd2d2ec;hpb=c5c1142fe4f977cce8799df2470a73064a3f59ba;p=rsem.git

diff --git a/README.md b/README.md
index 5c6943b..b93678d 100644
--- a/README.md
+++ b/README.md
@@ -46,6 +46,13 @@ To compile RSEM, simply run
    
     make
 
+For cygwin users, please uncomment the 3rd and 7th line in
+'sam/Makefile' before you run 'make'.
+
+To compile EBSeq, which is included in the RSEM package, run
+
+    make ebseq
+
 To install, simply put the rsem directory in your environment's PATH
 variable.
 
@@ -53,8 +60,10 @@ variable.
 
 C++, Perl and R are required to be installed. 
 
-To take advantage of RSEM's built-in support for the Bowtie alignment
-program, you must have [Bowtie](http://bowtie-bio.sourceforge.net) installed.
+To take advantage of RSEM's built-in support for the Bowtie/Bowtie 2
+alignment program, you must have
+[Bowtie](http://bowtie-bio.sourceforge.net) and/or [Bowtie
+2](http://bowtie-bio.sourceforge.net/bowtie2) installed.
 
 ## <a name="usage"></a> Usage
 
@@ -100,7 +109,13 @@ consideration.
 #### Using an alternative aligner
 
 By default, RSEM automates the alignment of reads to reference
-transcripts using the Bowtie alignment program.  To use an alternative
+transcripts using the Bowtie alignment program. Turn on '--bowtie2'
+for 'rsem-prepare-reference' and 'rsem-calculate-expression' will
+allow RSEM to use the Bowtie 2 alignment program instead. Please note
+that indel alignments, local alignments and discordant alignments are
+disallowed when RSEM uses Bowtie 2 since RSEM currently cannot handle
+them. See the description of '--bowtie2' option in
+'rsem-calculate-expression' for more details. To use an alternative
 alignment program, align the input reads against the file
 'reference_name.idx.fa' generated by 'rsem-prepare-reference', and
 format the alignment output in SAM or BAM format.  Then, instead of
@@ -279,7 +294,7 @@ to get usage information or read the following subsections.
 
 __reference_name:__ The name of RSEM references, which should be already generated by 'rsem-prepare-reference'   	     
 
-__estimated_model_file:__ This file describes how the RNA-Seq reads will be sequenced given the expression levels. It determines what kind of reads will be simulated (single-end/paired-end, w/o quality score) and includes parameters for fragment length distribution, read start position distribution, sequencing error models, etc. Normally, this file should be learned from real data using 'rsem-calculate-expression'. The file can be found under the 'sample_name.stat' folder with the name of 'sample_name.model'    
+__estimated_model_file:__ This file describes how the RNA-Seq reads will be sequenced given the expression levels. It determines what kind of reads will be simulated (single-end/paired-end, w/o quality score) and includes parameters for fragment length distribution, read start position distribution, sequencing error models, etc. Normally, this file should be learned from real data using 'rsem-calculate-expression'. The file can be found under the 'sample_name.stat' folder with the name of 'sample_name.model'. 'model_file_description.txt' provides the format and meanings of this file.    
 
 __estimated_isoform_results:__ This file contains expression levels for all isoforms recorded in the reference. It can be learned using 'rsem-calculate-expression' from real data. The corresponding file users want to use is 'sample_name.isoforms.results'. If simulating from user-designed expression profile is desired, start from a learned 'sample_name.isoforms.results' file and only modify the 'TPM' column. The simulator only reads the TPM column. But keeping the file format the same is required.   
 
@@ -430,7 +445,7 @@ be sent to <a href="mailto:nleng@wisc.edu">Ning Leng</a>.
 
 ## <a name="authors"></a> Authors
 
-RSEM is developed by Bo Li, with substaintial technical input from Colin Dewey.
+The RSEM algorithm is developed by Bo Li and Colin Dewey. The RSEM software is mainly implemented by Bo Li.
 
 ## <a name="acknowledgements"></a> Acknowledgements
 
@@ -439,9 +454,9 @@ 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 for contributing patches.
+We thank earonesty, Dr. Samuel Arvidsson for contributing patches.
 
-We thank Han Lin for suggesting possible fixes. 
+We thank Han Lin, j.miller for suggesting possible fixes. 
 
 ## <a name="license"></a> License