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However, accounting for that sex chromosome complement on the sample in quantifying gene expression has been constrained due to shared sequence homology between the sexual intercourse chromosomes, X and Y, that can confound gene expression estimates.
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Genomic analysis of many nonmodel species has uncovered an incredible range of sexual intercourse chromosome systems, making it possible to empirically test the rich body of evolutionary theory that describes each stage of intercourse chromosome evolution. Classic theory predicts that sexual intercourse chromosomes originate from a pair of homologous autosomes and recombination between them is suppressed by means of inversions to take care of sexual conflict. The resulting degradation in the Y chromosome gene content creates the need for dosage payment from the heterogametic sexual intercourse. Intercourse chromosome theory also implies a linear process, starting from sex chromosome origin and progressing to heteromorphism. Even with many convergent genomic patterns exhibited by independently progressed intercourse chromosome systems, and many case studies supporting these theoretical predictions, emerging data give a lot of interesting exceptions to those long-standing theories, and counsel that the remarkable range of intercourse chromosomes is matched by a similar range in their evolution.
We identified that when reads were aligned to some reference genome informed with the intercourse chromosome complement for both male XY and female XX tissue samples, reads around the X chromosome increased by ~ 0.
Transcript quantification for trimmed paired RNA-Seq brain cortex samples was believed twice, once to some default decoy-informed reference transcriptome index and once to the sex chromosome complement informed decoy-conscious reference transcriptome index using Salmon with the –validateMappings flag. Salmon’s –validateMappings adopts a scheme for finding protentional mapping loci of a read using a sequence algorithm released in minimap2 [45].
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Variation across populations in physical size on the Y chromosome; extent of Y differentiation and extent of nonrecombining regions.
sex chromosome, either of the set of chromosomes that determine whether someone is male or female. The sex chromosomes of human beings and other mammals are designated by researchers as X and Y.
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Human X and Y chromosomes share an evolutionary origin and, for a consequence, sequence similarity. We investigated whether the sequence homology between the X and Y chromosomes affects the useful source alignment of RNA-Seq reads and estimates of differential expression.
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