soap problem?

[semna]

Hi
I am working on soap analysis for pig genome. To identify alternative splicing I need to transform gtf or gff file to psl and id file. Anyone knows how can I do that? Thanks in advance.
reza

[RockChalkJayhawk]

Here is how I did it for the human genome.

Make PSL Annotation File
1. Go to table Browser in UCSC
2. Select RefSeq Genes track from Genes Group
3. Select RefSeqAli Table
4. Select Fields from primary and related tables
5. Click Get Output
6. Select all fields from hg19.refSeqAli EXCEPT bin
7. Also select geneName from hg19.refFlat fields
8. Save as Hg19.file
9. grep -v '#' Hg19.file|perl -ane '@arr=join("\t",@F[0..20]);print "@arr\n"'|sort >Hg19.psl
10. grep -v '#' Hg19.file|awk '{print $22"\t"$10}' |sort > ID.list