Indexing transcriptome bam file

[aayushraman]

I am using STAR/2.7.11b for the alignment step. I am using the following command

STAR --runMode alignReads --runThreadN 16 --genomeDir $star_index --outSAMattributes All --outFilterType BySJout --outFilterMultimapNmax 10 --outFilterMultimapScoreRange 1 --outFilterScoreMin 10 --outFilterMismatchNmax 5 --alignEndsType Local --outSAMtype BAM SortedByCoordinate --readFilesCommand zcat --outTmpDir $tempDIR --readFilesIn $R1 $R2 --quantMode TranscriptomeSAM GeneCounts --outFileNamePrefix sample1 \n

I am able to index the genome-based bam file but not the transcriptome bam file. What is the best way to index the transcriptome bam file? Thanks!