Hi,
I have the following GTF file (from Gencode):
I would like to change all "PGOMOU*" names for "ENSMUSG*". How it can be done in R or awk in an easy way? Sorry for naive question, but I am struggling with awk to make the changes in GTF file. PGOMOU* nomenclature is not recognized by Bowtie/TopHat. So, any input is welcome!
I have the following GTF file (from Gencode):
HTML Code:
chr10 Yale_UCSC transcript 3117806 3119013 . - . gene_id "PGOMOU00000268019"; transcript_id "PGOMOU00000268019"; gene_type "pseudogene"; gene_status "UNKNOWN"; gene_name "PGOMOU00000268019"; transcript_type "pseudogene"; transcript_status "UNKNOWN"; transcript_name "PGOMOU00000268019"; level 3; tag "2way_pseudo_cons"; yale_id "PGOMOU00000268019"; ucsc_id "NM_019986.3-3"; parent_id "ENSMUSG00000021476 "; chr10 Yale_UCSC transcript 3139466 3141067 . - . gene_id "PGOMOU00000268020"; transcript_id "PGOMOU00000268020"; gene_type "pseudogene"; gene_status "UNKNOWN"; gene_name "PGOMOU00000268020"; transcript_type "pseudogene"; transcript_status "UNKNOWN"; transcript_name "PGOMOU00000268020"; level 3; tag "2way_pseudo_cons"; yale_id "PGOMOU00000268020"; ucsc_id "BC036983.1-1"; parent_id "ENSMUSG00000028228 ";
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