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Where variation maps to transcripts from both genesets we define the variant annotation as 'concordant'concordant
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All intronic SNPs were mapped to transcripts and labeled according to whether they fell inside the first intron and by distance from the intron start site.
The KO IDs were mapped to transcripts annotated in AlgaePath.
However, the probes mapping to transcripts do not generally lead to new probesets being annotated.
Exactly how were these sequences mapped to transcripts to identify the exon combinations?
Reads mapping to transcripts from more than one gene were discarded.
Another challenge in transcriptomic analysis comes from the ambiguities in read/tag mapping to transcripts.
Overall, the majority of variants map to transcripts in both genesets.
Reads that mapped to transcripts of more than one gene or multiple times to a transcript were discarded.
All the tags previously unambiguously mapped to transcripts were removed from the initial list to avoid an overlap.
In the context of RNA-Seq, θ represents the average number of reads mapped to transcripts in a sample.
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