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Old 07-13-2010, 10:08 AM   #1
RockChalkJayhawk
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Location: Rochester, MN

Join Date: Mar 2009
Posts: 191
Default Hg19.PSL and SOAPals

All,

I'm trying our SOAPals for alternative splicing. However, it requires a PSL annotation file. I have a GTF file, but was wondering if anyone had a converter that goes from GTF to PSL?

I also don't understand what is meant by the -key requirement. This is very little documentation so far.

Has anyone else tried this?
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Old 07-14-2010, 10:22 AM   #2
RockChalkJayhawk
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Location: Rochester, MN

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Posts: 191
Default PSL Fix

After toying around with it for a while, this is what I came up with and it seems to work for making the PSL and ID files needed by SOAPals:

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
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