Extract features from an alignment

[Meritxell Riera Bellés]

Hi everyone, 

I'm trying to run Maffilter to extract CpG of a maf alignment generated with last and CpG coordinates from one of the two species in GFF, generated from a bed format. However, even though the program runs without specific errors, I don't get any matches. I believe that the format of the inputs provided is not correct. It would be very helpful if anyone that has used this filter could give me examples of the inputs provided and the output received. 

Thanks!!

[Julien Yann Dutheil]

Dear Meritxell,

A typical error is when the chromosome / contig id of the GFF file do not match the ones in the MAF file. Can you double-check that everything is correct there?

Note that the development version of MafFilter allows you to read Bed files directly (but you will need to compile it).

[Meritxell Riera Bellés]

Dear Julien,

I have set the same id in both the GFF and MAF files. Could you tell me which one is the development version of MafFilter? I've tried the last version I could find (1.1.2-1) and I get an error when providing a bed format. Thanks!

[Julien Yann Dutheil]

Dear Meritxell,

The development version is the one from the git repository. If you want, you can send me your maf/gff/option file and I can give them a look.

J.