Hi-
I am running cufflinks on mouse RNAseq with genes.gtf as reference file on the bam files that i generated using tophat2/bowtie. The output genes.fpkm_tracking and isoforms.fpkm_tracking have the following format:
tracking_id class_code nearest_ref_id gene_id gene_short_name tss_id locus length coverage FPKM FPKM_conf_lo FPKM_conf_hi FPKM_status
ENSMUSG00000090025 - - ENSMUSG00000090025 Gm16088 TSS82763 1:3054232-3054733 - - 0 0 0 OK
ENSMUSG00000064842 - - ENSMUSG00000064842 Gm26206 TSS81070 1:3102015-3102125 - - 0 0 0 OK
ENSMUSG00000025900 - - ENSMUSG00000025900 Rp1 TSS11475 1:4343506-4360314 - - 0 0 0 OK
However, I also want the column that enlists the gene biotype (pseudogene, protein coding..) that is in the gtf file i am using as reference. how can I incorporate this in the run? is it doable? I'd appreciate the help in this matter.
I am running cufflinks on mouse RNAseq with genes.gtf as reference file on the bam files that i generated using tophat2/bowtie. The output genes.fpkm_tracking and isoforms.fpkm_tracking have the following format:
tracking_id class_code nearest_ref_id gene_id gene_short_name tss_id locus length coverage FPKM FPKM_conf_lo FPKM_conf_hi FPKM_status
ENSMUSG00000090025 - - ENSMUSG00000090025 Gm16088 TSS82763 1:3054232-3054733 - - 0 0 0 OK
ENSMUSG00000064842 - - ENSMUSG00000064842 Gm26206 TSS81070 1:3102015-3102125 - - 0 0 0 OK
ENSMUSG00000025900 - - ENSMUSG00000025900 Rp1 TSS11475 1:4343506-4360314 - - 0 0 0 OK
However, I also want the column that enlists the gene biotype (pseudogene, protein coding..) that is in the gtf file i am using as reference. how can I incorporate this in the run? is it doable? I'd appreciate the help in this matter.