REFERENCE GENOME - merging files

Question

[GiuliaAC]

Hi!

I would like to create a new reference genome (host + other genes) for mapping transcriptomic data

In order to do this, I have the 2 .fa files and the 2 .gtf files

For fasta files, I can easly merge the files cat file1.fa file2.fa > file1.2.fa

And for gtf files? What can I do?

Thanks for the help

[Pierre Lindenbaum]

(cat f1.gtf && grep -v "^#" f2.gtf) > 1.2.gtf ?

[JC]

to extend this, it could be as simply concat both files, just be sure you have different chromosome names

[GiuliaAC]

How can I check it? And if they are not different, what can I do?

[GenoMax]

May be best to use agat_sp_merge_annotations.pl from AGAT a proper GTF/GFF tooklit.

[GiuliaAC]

I didn't know AGAT, thank you!