MPIWang2013 – Bur-0 and C24 Genome templates
While examining effects of transposons on gene expression, we built genome templates of Bur-0 and C24 using the paired-end reads published with MPISchneeberger2011. These reads give about 80x genome coverage and allowed prediction of transposon deletions in Bur-0 and C24 compared to Col-0.
We used the SHORE pipeline to align the reads to the Col-0 reference genome and extracted the consensus sequences as genome templates by calling bases with quality>24, support>6, concordance>0.7 and average hits = 1.
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