extracting exons and introns cordinates from the gtf file

Question

[HK]

Hi everyone,

I have a gtf file download from Gencode (##description: evidence-based annotation of the human genome (GRCh38), version 25 (Ensembl 85), ##provider: GENCODE) and now want to load this gtf in R or in linux and want to do few things

1) want to know how many exons per gene and the cordinates of these exons per gene (the file has the transcripts information als, but i only want per gene).

2) Extract the sequence of these exons (gene). I did try biomart and did get the cordinates and sequence of exons but for all transcripts of that gene.

3) Also want the intron cordinates.

Kindly i need suggestion which package should i use in R to upload my downloaded gtf file and perform the tas or maybe how should ui do this by linux commands.

[h.mon]

Probably the BioConductor package GenomicFeatures does everything (or almost) you need. Have a look at the function exonsBy().