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

[rsem.git] / README.md

diff --git a/README.md b/README.md
index bb66d5498be3014ccab93ef382d6d05536e6e047..6e8acd8fb2df0f100fc6a0622bde5467aa8b649a 100644 (file)
--- a/README.md
+++ b/README.md
@@ -102,17 +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.
-
-Some aligners' (other than Bowtie) output might need to be converted
-so that RSEM can use. For conversion, please run
+'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
+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