Modified 'convert-sam-for-rsem' so that this program will convert users' SAM/BAM...

[rsem.git] / README.md

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@@ -102,17 +102,24 @@ 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
-the alignment output in SAM or BAM format.  Then, instead of providing
-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.
+'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 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.

 
 RSEM requires all alignments of the same read group together. For
 paired-end reads, RSEM also requires the two mates of any alignment be
 
 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
+adjacent. To check if your SAM/BAM file satisfy the requirements,
+please run
+
+    rsem-sam-validator <input.sam/input.bam>
+
+If your file does not satisfy the requirements, you can use
+'convert-sam-for-rsem' to convert it into a BAM file which RSEM can
+process. Please run

  
    convert-sam-for-rsem --help
 
  
    convert-sam-for-rsem --help