One line fasta file with overlapped scaffold

[illinu]

Hi,

Is there a way to have these overlapped sequences fixed (attached)?
It only happens for a few scaffolds and I don't know why. I tried copying and pasting the sequence in another text viewer, the sequence pastes in multiline format and when transforming back to one line it again overlaps.

Cheers

[rhinoceros]

What text viewer are you using? Perhaps it has some predefined maximum line length and it doesn't really know what to do with the part that doesn't fit? What happens when you cat your file in the command line?

[illinu]

You are right, it has to be that since it happens in the two longest scaffolds. I use gedit. If I cat the file it displays multiline sequences, if I open with other editors (GVim, GNU Emacs 23) it does not read one line either, instead it displays all scaffolds in multiline.

[rhinoceros]

So there you have it, there's nothing wrong with your file..

[illinu]

Thank you rhinoceros