Hi everyone,
I have gone through the "tuxedo" RNA-seq analysis pipeline for rice data, and anything seemed to work well. But I am not sure how the "tracking_id" was generated, and how the coordinates were assigned for each tracking_id. Does the "tracking_id" come from the transcriptome assembly using the RNA-seq data?
I can find the "gene_short_name" for most of the "tracking_id" in the file "genes.fpkm_tracking", because of the gene annotation. But when I checked the corresponding coordinates for each "tracking_id" in the file "genes.fpkm_tracking", the coordinates seemed to be different from those of annotated genes by the genome sequencing consortium. So, how does this happen? Does it mean that the initial gene annotation was incorrect? How to solve this discrepancy when you have similar issues?
I really hope to get answers from cufflinks experts. Thank you for your patience!
I have gone through the "tuxedo" RNA-seq analysis pipeline for rice data, and anything seemed to work well. But I am not sure how the "tracking_id" was generated, and how the coordinates were assigned for each tracking_id. Does the "tracking_id" come from the transcriptome assembly using the RNA-seq data?
I can find the "gene_short_name" for most of the "tracking_id" in the file "genes.fpkm_tracking", because of the gene annotation. But when I checked the corresponding coordinates for each "tracking_id" in the file "genes.fpkm_tracking", the coordinates seemed to be different from those of annotated genes by the genome sequencing consortium. So, how does this happen? Does it mean that the initial gene annotation was incorrect? How to solve this discrepancy when you have similar issues?
I really hope to get answers from cufflinks experts. Thank you for your patience!
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