[Enrico Palazzo]

I am having problems with the combined.gtf from cuffcompare produced on a Linux system - gedit will not open the file, giving the error message

"gedit has not been able to detect the character coding.
Please check that you are not trying to open a binary file.
Select a character coding from the menu and try again."

The file will not load into the UCSC "tracks" with the error "Can't read file:"


It will load into emacs and openoffice - cutting and pasting from openoffice to gedit works - saving the file from gedit allows gedit to then open it.

Also will load into IGV

Seems like some non-ascii characters are being generated by cuffcompare. Any ideas why?

Thanks

Hi,
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