rsem-sam-validator <input.sam/input.bam/input.cram>
RSEM requires the alignments of a read to be adjacent. For paired-end reads, RSEM also requires the two mates of any alignment be adjacent. This tool checks if your SAM/BAM file satisfy the requirements.
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.
However, please note that RSEM does not support gapped alignments. So make sure that your aligner does not produce alignments with intersions/deletions. Also, please make sure that you use ‘reference_name.idx.fa’ , which is generated by RSEM, to build your aligner’s indices.