X-Git-Url: https://git.donarmstrong.com/?p=rsem.git;a=blobdiff_plain;f=README.md;h=b46826a58209fda36bc59cff8e860a95707dfe25;hp=a4c5ce504a0f284bb594e9a57807a17969a4fc51;hb=4a435fbee229af1dd5f76b4feb0ca71398ac8796;hpb=28196eb2a94c1585850189028fcaf7d51fbf68b8

diff --git a/README.md b/README.md
index a4c5ce5..b46826a 100644
--- a/README.md
+++ b/README.md
@@ -84,8 +84,8 @@ documentation page](http://deweylab.biostat.wisc.edu/rsem/rsem-calculate-express
 #### Calculating expression values from single-end data
 
 For single-end models, users have the option of providing a fragment
-length distribution via the --fragment-length-mean and
---fragment-length-sd options.  The specification of an accurate fragment
+length distribution via the '--fragment-length-mean' and
+'--fragment-length-sd' options.  The specification of an accurate fragment
 length distribution is important for the accuracy of expression level
 estimates from single-end data.  If the fragment length mean and sd are
 not provided, RSEM will not take a fragment length distribution into
@@ -96,12 +96,21 @@ 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
+'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
+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.
+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
+ 
+   convert-sam-for-rsem --help
+
+to get usage information or visit the [convert-sam-for-rsem
+documentation
+page](http://deweylab.biostat.wisc.edu/rsem/convert-sam-for-rsem.html).
 
 However, please note that RSEM does ** not ** support gapped
 alignments. So make sure that your aligner does not produce alignments