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Paired mappings with a distance > 1 kb were discarded, and paired reads with either only the forward or only the reverse read mapping were retained as single mapping reads.
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All of the configured data mapping and logical condition mapping are retained.
If a transcript was mapped to multiple genomic loci, then only the best mapping was retained; if more than one nearly identical best mapping existed (difference in BLAT scores < 5%), then the transcript was discarded to avoid ambiguity.
Although early visual experience is essential for the proper development of visual cortex, Striem-Amit et al. show that the underlying connectivity structure of retinotopic mapping is retained even in congenitally blind individuals.
For probes with multiple positive pools passing both tests, only those that are found on overlapping BAC clones of the preliminary map were retained.
The smoothing was done so that the noise was suppressed while the shape information from the depth maps was retained.
The marker order in the merged map was retained in the parental maps by inputting this as a fixed order to direct map generation, with progeny then analysed to detect double recombination events.
The positions of all uniquely mapping reads were retained.
Only uniquely mapping reads were retained and reads identified as PCR duplicates were discarded.
Among these, 21,152 mapped probes were retained after removing probes mapped with over 90% identity to multiple genes or mapped to sex chromosomes or mitochondrial DNA.
Next, the high-quality reads of 14 samples were mapped to the reference sequences by Bowtie2, and only uniquely mapped reads were retained for the following expression analysis by edgeR [ 34, 35] (Additional file 1).
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