Optimise STAR parameters to require only one STAR alignment

[joshua-biocoder]

Description of feature

Hi,

I was exploring this tool, and I see that you are using STAR alignment 3 times (for arriba, squid, and starfusion). Could you please explain the reason for using different STAR parameters for each of these tools? Also, please let me know if it's possible to optimize these parameters so that I can run STAR alignment only once and use the subsequent bam and chimeric file for all these 3 tools.

[rannick]

Hi,
If I knew already an optimal way, rnafusion would only align once! We have it on our list of priorities but a full assessment is needed, so in the meantime the alignment is done using arriba and STAR-fusion's recommendation (squid will be dropped). I can however point you in the direction of the STAR manual: https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf