How to build the STAR Genome index from the .gbk file?

Question

[lhaiyan3]

Dear all,

I need to build the STAR alignment Genome index file for my analysis. I have the .GBK file for my target sequence. I use the http://iubio.bio.indiana.edu/cgi-bin/readseq.cgi tools to change my .gbk file to .gff file, but it is not the standard format for the STAR required annotation.gtf format. I got the wrong message to run the STAR GenomeGenerate mode. Can anyone please give me some suggestions how to get the STAR required the gtf format from .gbk file? Thanks very much for your great help.

best

HY

Answer 1

[GenoMax]

To build a genome index you need to start with fasta formatted sequence file of the genome that you are interested in. If you only have genbank format file at hand then you should be able to use this utility to convert the file.

[WouterDeCoster]

If I understand OP correctly he want to create the index with (in addition to the fasta file) a transcript annotation file, which is why he aims to convert a gbk file to gtf/gff. However, it's unclear what goes wrong since OP was quite unspecific about the error message which was generated by STAR while trying to build the index with the generated gff file. So if OP could explain more (which error, which organism) we could troubleshoot more accurately.

[GenoMax]

Good point. Hopefully we will get clarification from OP.