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Old 04-07-2014, 04:41 AM   #5
kajot
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Location: Germany

Join Date: Dec 2013
Posts: 16
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I understand, I wasn't sure since in my .gtf file there are entries like this:

1 protein_coding exon 4830268 4830315 . + . exon_id "ENSMUSE00001118471"; exon_number "4"; gene_biotype "protein_coding"; gene_id "ENSMUSG00000025903"; gene_name "Lypla1"; p_id "P31648"; transcript_id "ENSMUST00000150971"; transcript_name "Lypla1-003"; tss_id "TSS49998";
1 protein_coding exon 4830268 4830315 . + . exon_id "ENSMUSE00001118471"; exon_number "4"; gene_biotype "protein_coding"; gene_id "ENSMUSG00000025903"; gene_name "Lypla1"; p_id "P31294"; transcript_id "ENSMUST00000119612"; transcript_name "Lypla1-009"; tss_id "TSS45053";


As you can see, there is a double entry for two transcripts from the same gene, but the exon position and gene IDs are the same, therefore I was a bit concerned that the script might count a read mapped to such exon twice for the same ENSMUSG00000025903.
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