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Reference genome and transcriptome informed by the intercourse chromosome complement from the sample increase capacity to detect sex differences in gene expression from RNA-Seq data
Variation across populations in physical size with the Y chromosome; extent of Y differentiation and extent of nonrecombining regions.
We located that using a reference genome with the sex chromosome complement of the sample resulted in higher measurements of X-linked gene transcription for both male and female samples and more differentially expressed genes about the X and Y chromosomes. We Furthermore investigated the use of a sexual intercourse chromosome complement informed transcriptome reference index for alignment-free quantification protocols. We observed no Y-linked expression in female XX samples only when the transcript quantification was performed using a transcriptome reference index informed about the sexual intercourse chromosome complement of your sample. We advise that future studies requiring aligning RNA-Seq reads to the reference genome or pseudo-alignment with a transcriptome reference should consider the sex chromosome complement of their samples previous to running default pipelines.
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Persons having two X chromosomes (XX) are female; folks having one X chromosome and one particular Y chromosome (XY) are male. The X chromosome resembles a large autosomal chromosome with a long as well as a short arm. The Y chromosome has a person long arm as well as a very short second arm. This path to maleness or femaleness originates at the moment of meiosis, when a cell divides to produce gametes, or intercourse cells having 50 % the normal number of chromosomes.
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We examined the differences and similarities in gene enrichment terms between the differentially expressed genes received from the differential expression analyses of your samples aligned on the default and intercourse chromosome complement informed reference genomes, to analyze Should the biological interpretation would change depending on the reference genome the samples were aligned to.
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b Using a standard alignment approach will result in reads misaligning between locations of high sequence homology to the sex chromosomes. c Using a reference genome that is informed with the genetic sexual intercourse in the sample may perhaps help to reduce misaligning between the X and Y chromosomes. In humans, samples without proof of the Y chromosome should be aligned to some Y-masked reference genome, and samples with proof of the Y should be aligned into a YPAR-masked reference genome
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