extract fasta sequence based on gene distance

Question

[yaghoub.amraei]

Hello everyone ... I have a cuffcompare output that has the same genes names and transcripts names, but the gene distance of each transcript is different with the same name. How can I get the fastasequence of any genes distance with the Bad Tools or GFF Read package?

1   Cufflinks   exon    58474   61195   .   +   .   gene_id "XLOC_000007"; transcript_id "TCONS_00022739"; exon_number "1"; gene_name "Os01g0101150"; oId "CUFF.865.1"; nearest_ref "Os01t0101150-00"; class_code "o"; tss_id "TSS17";
1   Cufflinks   exon    61423   61573   .   +   .   gene_id "XLOC_000007"; transcript_id "TCONS_00022739"; exon_number "2"; gene_name "Os01g0101150"; oId "CUFF.865.1"; nearest_ref "Os01t0101150-00"; class_code "o"; tss_id "TSS17";
1   Cufflinks   exon    61669   61794   .   +   .   gene_id "XLOC_000007"; transcript_id "TCONS_00022739"; exon_number "3"; gene_name "Os01g0101150"; oId "CUFF.865.1"; nearest_ref "Os01t0101150-00"; class_code "o"; tss_id "TSS17";
1   Cufflinks   exon    163041  164107  .   +   .   gene_id "XLOC_000015"; transcript_id "TCONS_00007850"; exon_number "1"; gene_name "Os01g0102850"; oId "CUFF.36.1"; nearest_ref "Os01t0102850-00"; class_code "o"; tss_id "TSS43";
1   Cufflinks   exon    163041  164107  .   +   .   gene_id "XLOC_000015"; transcript_id "TCONS_00007850"; exon_number "1"; gene_name "Os01g0102850"; oId "CUFF.36.1"; nearest_ref "Os01t0102850-00"; class_code "o"; tss_id "TSS43";

[rpolicastro]

Your GFF file is reporting exons, so for each line you have the genomic range for an exon of a particular gene. Do you want to get the sequence for each individual exon? Or do you want the sequence of the entire gene region on DNA?

[yaghoub.amraei]

my gold is LncRNA detection. The number of each line in the GTF file, of which I want to identify the LncRNA, is about 50,000 transcripts, and when I get the Festa file with GFF, I have about 17,000 transcripts. That is, GFFRID gives the Festa file based on a transcript, not based on the gene distance of each transcript.

[cpad0112]

getFasta function from bedtools might help you.

[yaghoub.amraei]

hello. amazing, as usual.