chromosome names in the annotations GTF file have to match chromosome names in the FASTA genome sequence files

[biounix]

According to the manual: chromosome names in the annotations GTF file have to match chromosome names in the FASTA genome sequence files

However, it seems that STAR ignores everything after the first space. So >chr1 This is chromosome one is as valid as just >chr1, and in the file chrName.txt both are shown as chr1.

I cannot find this behaviour documented, though.

Later, it's stated that The tabs are not allowed in chromosomes’ names, and spaces are not recommended. Why spaces are not recommended?

Thank you.

[biounix]

I just found it somehow documented here by @alexdobin: the "chromosome names" in the FASTA file (the string after ">" and before the first space) has to match the first field string in the GTF.

Which is in agreement with commonly accepted FASTA format specifications (ref1, ref2). It's surprising that there doesn't seem to be an official definition of the format (ref3).