Hi all,
I work on a single celled eukaryote whose genome has been sequenced. However the sequencing was not complete as there were several leftover scaffolds that contain more than a hunderd genes. Trying to get this information into cufflinks, I merged all these scaffolds toghether in one articial chromosomes with 4000N spacers in between scaffolds.
Alignement works great but I would like to use a GTF of this 'chromosome' with the original gene models to see if the gene models were substantially altered by cufflinks RABT. Is there a way where I could go from the FASTA files of the gene models to a GTF file for the 'new' chromosome? I could write a script but a pre-existing solution would be great as I am not a perl expert.
I work on a single celled eukaryote whose genome has been sequenced. However the sequencing was not complete as there were several leftover scaffolds that contain more than a hunderd genes. Trying to get this information into cufflinks, I merged all these scaffolds toghether in one articial chromosomes with 4000N spacers in between scaffolds.
Alignement works great but I would like to use a GTF of this 'chromosome' with the original gene models to see if the gene models were substantially altered by cufflinks RABT. Is there a way where I could go from the FASTA files of the gene models to a GTF file for the 'new' chromosome? I could write a script but a pre-existing solution would be great as I am not a perl expert.
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