X-Git-Url: https://git.donarmstrong.com/?p=rsem.git;a=blobdiff_plain;f=README.md;h=77c0693af045ab7daa551055dff244905bca111f;hp=bb66d5498be3014ccab93ef382d6d05536e6e047;hb=237bbdf363c9e42ee24e2fd63106dccf20d9bf2f;hpb=cb94fd597b180aa7cb01ae84c9d1025201b98d8e

diff --git a/README.md b/README.md
index bb66d54..77c0693 100644
--- a/README.md
+++ b/README.md
@@ -109,8 +109,10 @@ 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
+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
  
    convert-sam-for-rsem --help