Off topic:Using subtractbed(bedtools) to create intron gff

Question

[kousi31]

Hi all,

I have to extract intronic sequences from gff file (species - buffalo) to create training data set for CPAT. I am trying to do it with betools. Can anyone please tell me whether the following procedure is correct?

(ucsc table browser doesnot have sequences for buffalo, perl exttract_seq_from_gff3.pl -d genome.fa - gene_intron.gff3 > output_intron.fa from link also didnot work)

awk -F'\t' $3=='gene' my_gff >gene_gff

awk -F'\t' $3=='exons' my_gff >exon_gff`

subtractBed -a gene_gff -b exon_gff >intron_gff

fastaFromBed -fi genome.fa -bed intron.gff -fo intron.fa

Is there anyway to check if the regions in resultant intron gff/fa file is actually introns.

Please give me suggestions. Thanks in advance!