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This bias did not differ depending on whether the major allele was the reference allele or the alternate allele (Fisher's Exact Test, p = 0.28), supporting minimal read mapping biases in our data.
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Short RNA read mapping.
RB carried out short read mapping.
They comprised 142,825 reads mapping to unique loci and 176,135 reads mapping to multiple loci.
For read mapping, the minimal read coverage was set at 90% and the minimal alignment identity at 90%.
To evaluate the variation between the four independent experiments, we performed hierarchical sample clustering and a principal component analysis of the transcript profiles derived from read mapping on the minimal set of Arabidopsis coding sequences.
Around 92 98 % of the reads mapped to the zebrafish genome (Zv9) indicating minimal amount of degradation in the samples.
After read mapping, we discarded the reads mapped to multiple chromosomal positions and unmapped reads.
Summary of read mapping using Bowtie2.
INTRON: read mapping completely inside an intron.
To estimate mapping success, we quantified the total number of reads mapped and further distinguished between uniquely mapped reads and repetitively mapped reads.
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