Hello,

I have been trying to run calculate expression using rsem-calculate-expression from paired end reads. Here's the command I have been trying to run:

rsem-calculate-expression --star \
                           --star-path /home/apps/star/STAR-STAR_2.4.2a/bin/Linux_x86_64/ \
                           --star-gzipped-read-file \
                           --paired-end \
                           -p 16 \
                           sample1_R1.fastq.gz \
                           sample1_R2.fastq.gz \
                           ./refs/GRCh38 \
                           sample1_paired_end_quals

I get an error EXITING because of fatal error: buffer size for SJ output is too small. Solution: increase input parameter --limitOutSJcollapsed. Is there any way to change or add star parameters in RSEM? I am using RSEM v1.3.1.

Any help is much appreciated!