Thank you for sharing so many details! Very helpful.
For the immediate problem, the problem is likely with the fasta data formatting. Notice how the > title lines include description content after the identifier. STAR is really picky about the format and cannot isolate the chromosome identifier, which means it cannot “match it up” with the same chromosome identifier in the GFT data, then no lines are matched, so no exon lines are found.
Try this
- Run the tool NormalizeFasta on the custom genome fasta, being sure to check the box to remove everything after the first whitespace on the > title lines.
Optional
- I see a database assignment applied to your datasets. Database keys are fasta indexes.
- Did you create your own custom database key already? If so, you will need to delete the old one and recreate it with the normalized fasta file.
- In general is is not a good idea to assign a server database key to custom data since there could be small differences (mismatched fasta indexes).
- More details FAQ: How to use Custom Reference Genomes?
There are some important details I can’t see yet – the GTF format in the other columns specifically. The UCSC Table Browser will not output all of the data values that are sometimes needed. Instead, you will want the GTF from their downloads area (if available, sometimes you can request this, too) or from NCBI. This guide includes the details: FAQ: Extended Help for Differential Expression Analysis Tools
This recent topic has an example of getting the data from NCBI instead:
Let’s start there! Please try to get the fasta format simplified then we can help with the GTF data as needed. Thanks! 