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!
0 answers
No answers yet.
Log in to answer this question.
if you can get hold of the actual fasta sequence of those 'intron's you can check whether they all (or the vast majority) start with GT/GC and end in AG dinucleotide . This will give you a hint but is certainly not a bulletproof approach
Hello drkousi31!
Questions similar to yours can already be found at:
We have closed your question to allow us to keep similar content in the same thread.
If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.
Cheers!
In short, intron is the complement of intergenic and exonic regions. For a step-by-step tutorial, see: A: how to get intronic and intergenic sequences based on gff file?