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I downloaded the ensemble gtf file from UCSC browser. I find that some transcripts overlap > 90%. e.g. ENSBTAT00000001568 vs ENSBTAT00000046363. Therefore, if reads hit on the first, it will also hit the second. This will affect the gene expression analysis. Can we simply use one of them?
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Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.
The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
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