How to extract promoter coordinates from transcriptome.gtf file generated after cuffmerge ? file only has exon in annotation
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2.5 years ago
isha.lily20 ▴ 10

Hello

Can anybody tell me how to extract promoter coordinates from transcriptome.gtf file generated after cuffmerge result,

file only contains exon, or

is there any direct tool available ?

I am showing first 2 lines of my GTF file obtained after cuffmerge contain only exon

Chr1    Chr2    Chr3    Chr4    Chr5    Chr6    Chr7    Chr8    Chr9    Chr10   Chr11   Chr12   Chr13   Chr14   Chr15   Chr16   Chr17   Chr18   CUFF.1.2        tss_id  TSS1    
Chr1    Cufflinks   exon    3354    3616    .   +   .   gene_id XLOC_000001     transcript_id   TCONS_00000002      exon_number 2       oId CUFF.1.2        tss_id  TSS1

Thank you

cuffmerge promoter • 580 views
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