A piece of advice on subsetting genomes

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3.7 years ago

Begonia_pavonina ▴ 150

Hello everyone,

I have a piece of advice to ask rather than a specific technical question.

I have a genome from a non-reference organism, and a good annotation file in GFF format.

I used a blastn with another sequence to subset this genome, producing a FASTA file with the intersection of my genome and the other sequence. I have concatenated the results to get as many scaffolds as in my original FASTA file.

But now the annotation file positions are not matching anymore this genome subset.

What would you do? Try to write a script to adapt the new coordinates of the annotations to the genome subset? Or try to re-annotate the genome subset from scratch (with GMAP)? What would be the quicker way to do it on your opinion?

gff fasta genome annotations blast • 576 views

ADD COMMENT • link 3.7 years ago by Begonia_pavonina ▴ 150

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To be more clear, I try to transpose the range of the annotations file (GFF) from a big genome to a subset of the same genome.

I guess I will have to work with the GenomicRanges package on R.

But I still wonder if a Bedtools subcommand could do it as well?

ADD REPLY • link 3.7 years ago by Begonia_pavonina ▴ 150

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