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The raw reads obtained from Solexa sequencing were processed by summarizing data production, evaluating sequencing quality, calculating the length distribution of small RNA reads.
The sequence tags from the HiSeq sequencing were processed by a data-cleaning pipeline to get rid of the low-quality and too-small tags, as well as the adapter sequences from the tags.
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DAPI fluorescence was collected in a window from 438 485 nm Wild-type and mutant sequences were processed by the SwissModel server [40] in automatic mode, fixing as a template the A chain of 1PDQ (Drosophila Polycomb chromodomain complexed with the histone H3 tail containing trimethyl lysine 27 [3]).
The sequences were processed by removing vector sequences with Vector NTI Advance™ 10 program.
Masked sequences were processed by an in-house PERL script to produce vector-free sequences.
Sequences were processed by removing vector, adaptors and E. coli DNA sequences using CrossMatch [ 71].
Original sequences were processed by removing vector, adaptors and E. coli DNA sequences using CrossMatch [ 48].
After base calling, sequences were processed by using Phred [ 30, 31] to eliminate low quality sequences below Q20.
The resulting protein sequences were processed by scripts and R handling to retrieve the longest predicted ORF.
All raw sequences were processed by PHRED [ 50, 51] and screened for vector or Escherichia coli contamination.
Sequences were processed by CASAVA (Consensus Assessment of Sequence And VAriation), a propriety bioinformatics pipeline of Illumina, to obtain variant sets.
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