The order of @SQ tags in SAM/BAM files can be arbitrary now

[rsem.git] / README.md

diff --git a/README.md b/README.md
index bb66d5498be3014ccab93ef382d6d05536e6e047..77c0693af045ab7daa551055dff244905bca111f 100644 (file)
--- 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