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To remove quality variation caused by the block-switching effect, it is processed with the long window mode only.
With this distinction, it seems appropriate from the results of the analyses to remove Quality from Reaction and make it a separate category at the same level as Reaction.
The corresponding QUAL file also was updated to remove quality scores from reads not passing quality filters.
The median value of each spot on the array was considered and the probes were filtered to remove quality and factory controls.
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There is an intentionally anonymous, once removed quality to much of the work here.
Data analysis: The reads were processed using the fastx toolkit to remove low quality reads and trim low quality bases.
Unaligned and ambiguous reads were then quality trimmed removing low quality ends.
We then use PRINSEQ (Schmieder and Edwards, 2011) for read-based quality control, removing low quality and complexity reads and performing 3′end trimming.
Raw reads quality was visually inspected by means of FastQC software68 and then processed to remove low quality bases and contaminants (Illumina adapters).
This tool analyses images and clusters intensities and filters them to remove low quality data.
The reverse reads were processed with a BWA style trimming script to remove low quality sequences.
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Justyna Jupowicz-Kozak
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