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The isolated fragments were sequenced from both ends on the Illumina GAII platform, using 76 cycles for each read.
Then, 33-mer sequences were obtained after trimming the three-base index for each read.
Sequencing reagents for each read were pooled prior to loading.
For each read Rr we once again construct multiple alignments from the new set of reads in Rr.
However there is a fixed ceiling for each read length, due to the repeat structure of long repeats in genomes.
First, using multiple indexes of the reference genome, BFAST identifies candidate alignment locations (CALs) for each read.
The two libraries tags were mapped to the Human genome (Ensembl database) allowing up to three mismatches for each read.
For each read set, the KL divergence values are computed and then an average is taken over all read sets.
Mosaik examines all possible mapping locations for each read.
Such plot was built for each read individually.
No more than two mismatches were allowed in the alignment for each read.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com