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.
-
-Some aligners' (other than Bowtie) output might need to be converted
-so that RSEM can use. For conversion, please run
+'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
+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
to get usage information or visit the [convert-sam-for-rsem
documentation
projects / rsem.git / blobdiff