#37 Problem creating genewise sync file

[Pablo Deschepper]

Hi,

I have encountered a problem while creating a "genewise sync file" in order to calculate genewise Fst values with Popoolation2. I get the following error when running the script "all features of a gene have to be on the same strand; Problem for BG8813770 at /mnt/c/Popoolation_software/popoolation2/create-genewise-sync.pl line 334, <$ifh> line 153824." But when I look at that location, every features seems to be on the + strand so I don't see the problem (see attached image).

Kind regards,
Pablo

[Pablo Deschepper]

I see that everyting is on the + strand, but 2 exon and 2 CDS sequences are on the - strand. So this might be causing the error. Any suggestions on how to resolve this issue?

https://drive.google.com/open?id=1G8eQ-T_YBRavZRY9KIWER5Si7m58XmYo

[Arijit Ghosh]

Hi, I guess it wpuld have been solved by now, still just saying, delete that entry manually from the gtf file, and check that region manually.

[Maria Cortazar Chinarro]

Hi,
I am currently having the same error when I am running the script,
the following line is not valid at /sw/apps/bioinfo/popoolation2/1201/rackham/create-genewise-sync.pl line 232, <$ifh> line 360233.
Parsing gtf file..
Anyone knows how I can solve the problem?