Change STAR Parameters in rsem-calculate-expression

Question

[patelk26]

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!

Answer 1

[swbarnes2]

I think the STAR parameters are hard coded, you'd have to find where they are in the program, and change them. You can also run star on it's own, and have rsem work on the transcript.bam that star outputs.

Answer 2

[Jeremy Leipzig]

You may want to try a newer version of STAR - that error seems to be a bit of a relic. Truwl.com hosts the GTEX v10 pipeline which uses STAR 2.7.9a with RSEM 1.3.3.