Hi,

For alignment, I use BWA aligner. So after installing this tool I have generated the BWA index. For this purpose I use chromFa.tar.gz from ucsc website. Now, it works properly and I got my SAM files. But these SAM files are input in other simulation tool and for this simulation I need using these SAM files with same version annotation file in GTF format. My question is how to find exactly same version annotation file relate to chromFa.tar.gz? I have to say that I generate GTF file from UCSC but it is not exactly same version annotation file relate to chromFa.tar.gz

I appreciate if anybody share his/her comment with me