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After they reliably made these responses, scripts were removed from the recorders and then recorders were removed.
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Sequence reads from all samples were cleaned using the FASTX toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). First all the reads containing 'N' were discarded using a perl script, then adapter sequences were removed using the fastx_clipper program, followed by removal of quality < 5 bases from the 3′ end with fastq_quality_trimmer, requiring a minimum sequence length of 50 bp.
The protein alignments were back-translated into nt sequences using a perl script and all gaps were removed.
Reads above 30x coverage as well as singletons (likely to contain sequence errors and MDA artifacts) were removed (khmer scripts: normalize-by-median.py -C 30 -k 30; filter-abund.py).py
Redundant entries were removed using Shell scripts.
Homopolymer tracts and adaptors were removed using perl scripts as well as by manual examination.
Pure reads were demultiplexed and sequencing artifacts, including reads containing adapter and primer sequence, were removed using custom scripts.
Raw sequences [ 10] were retrieved in a FASTQ formatted file and the adapter sequences were removed using Perl Scripts.
A total of 4,388,665 20-25nt raw sequences were retrieved in a FASTQ formatted file and the adapter sequences were removed using Perl Scripts.
Low quality sequences and vector/adaptor contaminants were removed using custom scripts available from http://code.google.com/p/atgc-illumina/.
There were several scenes throughout this episode that were removed from the script, and not broadcast.
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