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An open-circuit respiratory device was used to measure the concentrations of O2 and CO2 in the outflowing air captured by a silicon face mask (reference No. 0, Glaxo Wellcome, Les Ulis, France) attached to a pneumotachograph (Statice Santé® Corp., Besançon, France).
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To avoid noise from these repeated elements, a repeat masked reference genome was used.
A SNP masked reference genome was used for alignment of the reads.
Repeat masked information was obtained from NCBI (reference genome and repeat masked reference genome: ftp://ftp.ncbi.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Sus_scrofa/Sscrofa10.2/Primary_Assembly/assembled_chromosomes/FASTA/) and merged with the repeat masked information used in Groenen et al. [ 39].
First, we employed mrsFAST [ 53], an exhaustive mapping tool that allows paralog detection, to align reads (allowing 6 mismatches) against the repeat masked reference genome; repeat mask information was obtained from NCBI.
To calculate the average read depth from those libraries, reads were first aligned to the repeat masked reference genome (Sus scrofa build 10.2) using mrsFAST v2.3.0.2 ("Micro-read (substitutions only) fast alignment and search tool" [ 49]) with an edit distance of at most 7 given that the mean divergence between the seven species is maximum 2% [ 39, 31].
As part of the blinded post hoc analysis for Down syndrome in our previous report, the z-scores were based on GC normalization and use of a repeat masked reference genome post alignment, in order to more accurately reflect the mappable genome from each chromosome.
Figure 3d displays the alias-free WD (AF-WD) [55] of the output signal of our filter with the above TCR mask and reference IF distribution, demonstrating that the quadratic phase component is separated by the proposed filter.
Superiority of the new network becomes more obvious when we mask the reference linkages derived from the term "protein synthesis".
To model this we mask the reference genome in silico based on restriction sites (e.g., C'CGG for MspI).
The averaged density was projected onto a mask in reference position (command AVERAGE), then expanded onto masks in n.c.s.-related positions (command EXPAND).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com