Fixed a bug related to intermediate output displaying in EM.cpp

[rsem.git] / README.md

diff --git a/README.md b/README.md
index 77c0693af045ab7daa551055dff244905bca111f..6e8acd8fb2df0f100fc6a0622bde5467aa8b649a 100644 (file)
--- a/README.md
+++ b/README.md
@@ -102,19 +102,26 @@ consideration.
 By default, RSEM automates the alignment of reads to reference
 transcripts using the Bowtie alignment program.  To use an alternative
 alignment program, align the input reads against the file
 By default, RSEM automates the alignment of reads to reference
 transcripts using the Bowtie alignment program.  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 providing
-reads to 'rsem-calculate-expression', specify the '--sam' or '--bam' option
-and provide the SAM or BAM file as an argument.  When using an
-alternative aligner, you may also want to provide the '--no-bowtie' option
-to 'rsem-prepare-reference' so that the Bowtie indices are not built.
+'reference_name.idx.fa' generated by 'rsem-prepare-reference', and
+format the alignment output in SAM or BAM format.  Then, instead of
+providing reads to 'rsem-calculate-expression', specify the '--sam' or
+'--bam' option and provide the SAM or BAM file as an argument.  When
+using an alternative aligner, you may also want to provide the
+'--no-bowtie' option to 'rsem-prepare-reference' so that the Bowtie
+indices are not built.

 
 RSEM requires all alignments of the same read group together. For
 paired-end reads, RSEM also requires the two mates of any alignment be
 
 RSEM requires all alignments of the same read group together. For
 paired-end reads, RSEM also requires the two mates of any alignment be

-adjacent. If the alternative aligner does not satisfy the first
-requirement, you can use 'convert-sam-for-rsem' for conversion. Please run
+adjacent. To check if your SAM/BAM file satisfy the requirements,
+please run
+
+    rsem-sam-validator <input.sam/input.bam>
+
+If your file does not satisfy the requirements, you can use
+'convert-sam-for-rsem' to convert it into a BAM file which RSEM can
+process. Please run

  
  

-   convert-sam-for-rsem --help
+    convert-sam-for-rsem --help

 
 to get usage information or visit the [convert-sam-for-rsem
 documentation
 
 to get usage information or visit the [convert-sam-for-rsem
 documentation