X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=README.md;h=6e8acd8fb2df0f100fc6a0622bde5467aa8b649a;hb=f67ec16ff8add74c17df026f77cf39e5a1aca051;hp=bb66d5498be3014ccab93ef382d6d05536e6e047;hpb=229ba9d68e0a801907631887640ab475d51c560c;p=rsem.git

diff --git a/README.md b/README.md
index bb66d54..6e8acd8 100644
--- 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
-'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