updated some description

[rsem.git] / README.md

diff --git a/README.md b/README.md
index a4c5ce504a0f284bb594e9a57807a17969a4fc51..b46826a58209fda36bc59cff8e860a95707dfe25 100644 (file)
--- 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
 #### 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
 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
 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
 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
 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
 
 However, please note that RSEM does ** not ** support gapped
 alignments. So make sure that your aligner does not produce alignments