problem for finding relative Version GTF file for my .fa file

Question

[modarzi]

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

[GenoMax]

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

How did that happen? Did you not use the same genome build when you made the GTF file (I assume using table browser)?

[modarzi]

Hi,

Thanks for comment. My simulation tool is CIRI2. when I used GTF file from UCSC, I found right CircRNA with nonsense gene Id. This problem relates to version of my GTF.

in following you can find my parameter setting in UCSC for getting GTF file:

clade: Mamal,

genome: Human,

assembly: Feb.2009(GRCh37/hg19),

group: Genes and gene predictions,

table: RefSeq All(ncbiRefSeq),

region: genome

I appericiate if you share your comment with me.

Best Regards

Mohammad