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  • #16
    Originally posted by [email protected] View Post
    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

    Comment

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