Sat, 10/18/2014 at 2:19 PM
Customer: We are working with plant genomic data. Datasets that we have: 1) RNA-Seq data from progenies of (P. d x P. t) cross, 2) Reference genome of P. t, and 3) Illumina resequencing of P. d genome.
Sun, 10/19/2014 at 4:24 PM
AccuraScience LB: Is the P. d genome expected to be very close to that of P. t, so that a reference genome of P. d can be obtained by routine SNV and Indel calling using the resequencing data you referred to, against the existing reference genome of P. t? Or a de novo assembly of the P. d genome has to be performed? A different way of phrasing this question is, are the differences between the two species expected to be mostly SNVs and Indels, or larger scale structural differences are expected to have occurred between them?
Strictly speaking, a reference genome is not absolutely required for us to do the transcriptome analysis (prior to the eQTL analysis). In case a good reference genome cannot be obtained for P. d genome, we can attempt to do a de novo assembly of the transcriptomes. We need to think about whether there is a way to take advantage of the available P. t reference genome, without introducing bias towards one of the two parent species when analyzing the progeny RNA-seq data.
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Note: LB stands for Lead Bioinformatician. An AccuraScience LB is a senior bioinformatics expert and leader of an AccuraScience data analysis team.
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