Question: I have a list of chromosomes, positions, gene ids, and transcript ids (from a gencode GTF file) - how can I get their corresponding REF and ALT values?
0
gravatar for claudiadast
14 months ago by
claudiadast0 wrote:

I have the latest Gencode GTF file filtered down to just the rows with exon information, that looks like the following:

chr1    HAVANA  exon    65419   65433       +       gene_id "ENSG00000186092"; transcript_id "ENST00000641515"; gene_type "protein_coding"; gene_name "OR4F5"; transcript_type "protein_coding"; transcript_name "OR4F5-202"; exon_number 1; exon_id "ENSE00003812156"; level 2; protein_id "ENSP00000493376"; tag "RNA_Seq_supported_partial"; tag "basic"; havana_gene "OTTHUMG00000001094"; havana_transcript "OTTHUMT00000003223";
chr1    HAVANA  exon    65520   65573       +       gene_id "ENSG00000186092"; transcript_id "ENST00000641515"; gene_type "protein_coding"; gene_name "OR4F5"; transcript_type "protein_coding"; transcript_name "OR4F5-202"; exon_number 2; exon_id "ENSE00003813641"; level 2; protein_id "ENSP00000493376"; tag "RNA_Seq_supported_partial"; tag "basic"; havana_gene "OTTHUMG00000001094"; havana_transcript "OTTHUMT00000003223";
chr1    HAVANA  exon    69037   71585       +       gene_id "ENSG00000186092"; transcript_id "ENST00000641515"; gene_type "protein_coding"; gene_name "OR4F5"; transcript_type "protein_coding"; transcript_name "OR4F5-202"; exon_number 3; exon_id "ENSE00003813949"; level 2; protein_id "ENSP00000493376"; tag "RNA_Seq_supported_partial"; tag "basic"; havana_gene "OTTHUMG00000001094"; havana_transcript "OTTHUMT00000003223";

I'm trying to turn this file into one that will have the columns Chromosome, Position, Ref, Alt, Gene, Transcript - how can I get the corresponding Ref and Alt values based on the gencode input file above?

gencode genome • 364 views
ADD COMMENTlink written 14 months ago by claudiadast0
1

Hello claudiadast ,

could you please explain why you like to do this? GTF have no information about REF and ALT. It just describes a certain feature (in your case "exon") in a given region.

fin swimmer

ADD REPLYlink written 14 months ago by finswimmer13k

Hi, yes I know, but I thought the GTF still gives me sufficient information (Gene, chromosome, position) to look up REF and ALT online.

ADD REPLYlink written 14 months ago by claudiadast0

Hello again,

it is still not clear what you are trying to do and why. Please descibe this to get proper help.

Thanks!

fin swimmer

ADD REPLYlink written 14 months ago by finswimmer13k
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