Hi,friends.I am trying to detect LncRNA from the GTF file prodused by the cufflinks.Some categories like this: chr1 Cufflinks exon 976045 976260 . + . gene_id "XLOC_000010"; transcript_id "TCONS_00000019"; exon_number "3"; gene_name "AGRN"; oId "CUFF.30.2"; nearest_ref "NM_198576"; class_code "j"; tss_id "TSS16"; chr1 Cufflinks exon 976553 976777 . + . gene_id "XLOC_000010"; transcript_id "TCONS_00000019"; exon_number "4"; gene_name "AGRN"; oId "CUFF.30.2"; nearest_ref "NM_198576"; class_code "j"; tss_id "TSS16"; chr1 Cufflinks exon 976858 977082 . + . gene_id "XLOC_000010"; transcript_id "TCONS_00000019"; exon_number "5"; gene_name "AGRN"; oId "CUFF.30.2"; nearest_ref "NM_198576"; class_code "j"; tss_id "TSS16"; If these are the result of my filter,shell I think I get three LncRNA?If the answer is yes I will comfuse the consistent transcript_id.If not,how shell I deal with it. Treat it as just one LncRNA from 976045 to 977082?
The another question is I download a bed file contains the information about the known LncRNA from noncode database,And I want to know which LncRNAs contain in my NGS data.I have two choices.First,just to see the "chr start end" of the bed file and the GTF File.Second,turn the two files to fasta format and blast.Which one is better?If the former, some LncRNA just have part but not all overlap with a transcript,shell I think the LncRNA contains in my data? I am a freshman and my questions maybe common sense to others.Really appreciate for your reply. best regard
Why do you think that exons in your GTF are from lncRNA?
gene_name "AGRN" - is protein coding (Ensembl).