5 months ago by
It looks like the BLASTN job failed, so that cannot be used as input Star-Fusion. My guess is that the failure is due to the fasta identifier lines containing description content (is not formatted correctly for a custom genome).
Also, the fasta reference supplied does not appear to be based on the same rat genome/build as the reference annotation dataset, so even if you had BLASTN succeed, a genome mismatch problem would later come up with Star-Fusion.
genes.gft annotation you is from iGenomes and from one of the UCSC builds they host (
rn6) -- correct? These genome build/versions are all natively indexed for Star-Fusion already at Galaxy Main https://usegalaxy.org, so there is no need to do the BLASTN step.
Solution: Use the option Source for sequence to search > Locally cashed sequences and set the
rnX version to be the same genome build/version as the source for the
Support FAQs: https://galaxyproject.org/support/
Thanks! Jen, Galaxy team