Hi
I tried to look online on various forums for this problem, unfortunately could not seek much help.
1. From my cufflinks output, for the various genes, I was trying to find their corresponding gene biotype and I was successful in doing it. I used the genes.fpkm_tracking file and the gtf file from ensembl, and I found out the whether my genes are protein coding or non coding genes. But can anyone tell me how to go about doing this at the transcript level. How do I find if my transcripts are protein_coding or ncRNA and if ncRNA, whether they are antisense, pseudogene, miRNA,etc.
2. Is there an annotation file which would give me information on the transcript biotype - can someone suggest me please.
Because when I use this annotation - Mus_musculus.GRCm38.71.gtf : This file only gives me the gene_biotype and not the transcript_biotype.
GL456350.1 protein_coding exon 993 1059 . - . gene_id "ENSMUSG00000094121"; transcript_id "ENSM UST00000177695"; exon_number "1"; gene_name "Ccl21c"; gene_biotype "protein_coding"; transcript_name "Ccl21c-201"; exon_id "ENSMUS E00000980949";
Any help in this regard will be highly appreciated. Thanks in advance.
I tried to look online on various forums for this problem, unfortunately could not seek much help.
1. From my cufflinks output, for the various genes, I was trying to find their corresponding gene biotype and I was successful in doing it. I used the genes.fpkm_tracking file and the gtf file from ensembl, and I found out the whether my genes are protein coding or non coding genes. But can anyone tell me how to go about doing this at the transcript level. How do I find if my transcripts are protein_coding or ncRNA and if ncRNA, whether they are antisense, pseudogene, miRNA,etc.
2. Is there an annotation file which would give me information on the transcript biotype - can someone suggest me please.
Because when I use this annotation - Mus_musculus.GRCm38.71.gtf : This file only gives me the gene_biotype and not the transcript_biotype.
GL456350.1 protein_coding exon 993 1059 . - . gene_id "ENSMUSG00000094121"; transcript_id "ENSM UST00000177695"; exon_number "1"; gene_name "Ccl21c"; gene_biotype "protein_coding"; transcript_name "Ccl21c-201"; exon_id "ENSMUS E00000980949";
Any help in this regard will be highly appreciated. Thanks in advance.