Originally posted by [email protected]
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I had the same problem with cuffcompare. I think cuffcompare generates illegal symbols if the strand orientation is unknown. Do you have entries like "^@" in the 7th column?
I fixed it with:
awk -F "\t" '{if ($7!="+" && $7!="-") print $1 "\t" $2 "\t" $3 "\t" $4 "\t" $5 "\t" $6 "\t" "." "\t" $8 "\t" $9 "\t" $10; else print $0}' stdout.combined.gtf > fixed.gtf
Looks ugly but for me it works
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