X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=README.md;h=77c0693af045ab7daa551055dff244905bca111f;hb=97554bbac838f2ed578d81f98e421dac0669e74e;hp=bb66d5498be3014ccab93ef382d6d05536e6e047;hpb=229ba9d68e0a801907631887640ab475d51c560c;p=rsem.git

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