Dear RSEM group,
I am following star-rsem pipeline, where I aligned the using star with the following options-
--outSAMunmapped Within \
--outFilterType BySJout \
--outSAMattributes NH HI AS NM MD \
--outSAMtype BAM Unsorted \
--quantMode TranscriptomeSAM GeneCounts \
Then I ran RSEM, suing the Aligned.toTranscriptome.out.bam file, a sample script used for RSEM quatification is given below.
rsem-calculate-expression -p 8 --paired-end --alignments \
--ci-memory 32000 \
--seed 123456 \
--strandedness reverse \
$bam db/refanno/ensembl_rsem $out > $log
So, my question is -Do I need to sort the bam files before running RSEM quantification?
I also learned from Harvard edx tutorial that RSEM needs and exon only file for successive running.
So next question is do I need to make exon only gtf file in/for the above steps I see that RSEM alignment requires exon only gtf.
Thank you for your time and consideration.