Hello to all,
I hope everyone is well! I want to ask if anyone knows if there are any parameters in STAR that prevent the alignment of reads to unannotated splice junctions? I want to speed the alignment task by limiting alignments to splice junctions that are not known. I already included --sjdbScore to 0, --alignSJoverhangMin to 10. But, it still takes some time and I still get splices that for the moment don't interest me.
Thanks in advance for your comments!