Identification of Domains altered by alternative splicing

Question

[mail2steff]

I am analyzing alternative splicing (AS) events in my samples. I need to find out the functional domain which is altered by AS. When I tested ASTAFUNK with sample data, it worked fine.

I have genome annotation file (GTF file generated from cufflinks output) for my samples. But when I tried ASTAFUNK, I am getting java.lang.NullPointerException. Is there any problem with the GTF file? Could you please let me know where I have gone wrong. I have attached example format of my sample GTF file

1 Cufflinks transcript 3631 5899 1000 + gene_id "AT1G01010"; transcript_id "AT1G01010 1"; FPKM "6 7317774810"; frac "1 000000"; conf_lo "5 813365"; conf_hi "7 650190"; cov "7 446027"; full_read_support "yes";
1 Cufflinks exon 3631 3913 1000 + gene_id "AT1G01010"; transcript_id "AT1G01010 1"; exon_number "1"; FPKM "6 7317774810"; frac "1 000000"; conf_lo "5 813365"; conf_hi "7 650190"; cov "7 446027";

Answer 1

[vitorlimac2]

Hi mail2steff ,

sorry for this late answer.

For the lastest version, you can obtain the source code or obtain the lastest binaries

More specific questions can be found here: http://astafunk.sammeth.net