Hi,
Is there a tool to create a fasta file using the long gene length sequence (i.e., TSE to TSS) that includes all the genomic elements, including 5' UTR, exons, introns 3'UTR from hg38? And then create a new gtf file using the fasta file subset and original gtf file information?
Thank you!
2 answers
Juke34 I have another question. Is there a way to extract the longest gene sequence without the introns? For example:
agat_sp_extract_sequences.pl -g infile.gff -f infile.fasta -t exon, but I want the sequence in the gene level and not in the transcript level. Thanks a lot!
Hi, You can use bedtools' getfasta function to extract a sequence from a fasta file, creating a new fasta. Since you work with human, you should have the complete fasta and gene information at hand. Just create a bed file (I guess gtf works as well) with only start and end of your long gene.
bedtools getfasta -fi hg36.fasta -bed myGene.bed -fo myGene.fasta
Then take the original gtf and reduce all coordinates by the one from your bed file (check for 0-based vs. 1-based coordinates in bed vs. gtf ). Adjust the contig name if necessary and load everything into IGV and check if it fits.
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