Question: Hi everyone !

I'm still struggling on maker.

What I want to do, is to follow step by step the maker tutorial for Snap training (the one described here : http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial#Training_ab_initio_Gene_Predictors ).

My input file is an genome assembly I made, with several contigs.

In the maker tutorial, they ask to convert the generated gff into a zff, and some other task. My problem is that, in the tutorial, they are working only on one locus, or one file. But in my results, I have like thousands of directories, each one containing several gff.

For example :

Loutre:~/Documents/maker/cleaned_suzukii_90_size.maker.output/cleaned_suzukii_90_size_datastore$ ls
00 0B 16 22 2D 38 43 4F 5A 66 71 7C 87 92 9D A9 B4 BF CA D5 E0 EB F6
(...) DF EA F5

And each directory could possibly contain several subdirectories, but the number can vary from one to another :

Loutre:~/Documents/maker/cleaned_suzukii_90_size.maker.output/cleaned_suzukii_90_size_datastore$ cd 0B/
Loutre:~/Documents/maker/cleaned_suzukii_90_size.maker.output/cleaned_suzukii_90_size_datastore/0B$ ls
28 67 7C 92 D0 F8
Loutre:~/Documents/maker/cleaned_suzukii_90_size.maker.output/cleaned_suzukii_90_size_datastore/0B$ cd 28
Loutre:~/Documents/maker/cleaned_suzukii_90_size.maker.output/cleaned_suzukii_90_size_datastore/0B/28$ ls
tig00000634
Loutre:~/Documents/maker/cleaned_suzukii_90_size.maker.output/cleaned_suzukii_90_size_datastore/0B/28$ cd tig00000634/
Loutre:~/Documents/maker/cleaned_suzukii_90_size.maker.output/cleaned_suzukii_90_size_datastore/0B/28/tig00000634$ ls
run.log
theVoid.tig00000634
tig00000634.gff
tig00000634.maker.augustus_masked.proteins.fasta
tig00000634.maker.augustus_masked.transcripts.fasta
tig00000634.maker.non_overlapping_ab_initio.proteins.fasta
tig00000634.maker.non_overlapping_ab_initio.transcripts.fasta

The ones I'm interested in are the simple tig00(number).gff, but I want to train snap for each contig like this, I want to train snap for the whole assembly, and I hope that I don't have to do this for each .gff file, even if a script do it for me... Because the folowing steps for Snap trainign require to launch maker again, with the hmm model produced by SNap on the whole genome.

What I want, is a easy way to convert all theses gff to only one output gff, which correspond to the maker output. I can't find something looking like this in the maker documentation, but I'm sure that maker users know a way to do what I want.

Do you have any advices ? Thanks for your help !

Cheers,

Roxane

Answer: You can merge all gff3 files from the MAKER output using the gff3_merge script that comes with MAKER -

there should be a file ending in index.log in the uppermost folder with your output data, let's call it example_index.log

gff3_merge -d example_index.log

This will merge *all* of the output into one gigantic gff3 file (repeatmasker results, alignments, various ab initio predictors etc.). This will also print the fasta sequences into the end of the gff3 file (use -n to stop that behaviour). If you want the MAKER gene models only use the -g flag, or use grep to search for any other data sources.

Looks like you can use the maker2zff script in the same way, then you can skip gff3_merge:

maker2zff -d example_index.log

(You should probably check the filtering options of that script to get better gene models, but the defaults look pretty stringent already)