Question: Identification of Domains altered by alternative splicing
2
gravatar for mail2steff
2.7 years ago by
mail2steff60
Potsdam, Germay
mail2steff60 wrote:

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";

ADD COMMENTlink modified 22 months ago by vitorlimac20 • written 2.7 years ago by mail2steff60
0
gravatar for vitorlimac2
22 months ago by
Rio de Janeiro, Brazil
vitorlimac20 wrote:

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

ADD COMMENTlink modified 22 months ago • written 22 months ago by vitorlimac20
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