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During this procedure, all low quality reads were removed, such as reads with 3′ and 5′ adapter contaminants, those without insert tags, and those with poly A sequences.
The reads shorter than 18 nucleotides, containing 5′ primer contaminants, containing poly A tail or missing 3′ primer, and insert tags were also excluded from the data sets.
The workflow for obtaining 'clean' reads involved filtering low quality tags; removing raw reads with 5' primer contaminants; trimming 3' adaptors; removing reads without insert tags; discarding reads with polyA tails; and removing contaminants formed by adaptor adaptor ligation.
After discarding the sequences shorter than 18 nt, eliminating low-quality sequences and removing contaminants formed by adapter adapter ligation, reads without 3′ ligation and insert tags were obtained.
All raw sequencing data was processed using the SOAP software (BGI Company) to obtain clean reads from each library as follows: except for low quality reads, reads with 5′ primer contaminants, reads without a 3′ primer, reads with no insert tags, reads with poly A tags, reads shorter than 18 nt and longer than 30 nt.
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Low quality reads, reads without the adaptors, reads with polyA sequences and reads without the insert tag where removed.
After excluding low quality reads, reads with 5' primer contaminants, reads without 3' primer, reads without the insert tag, and reads shorter than 18 nt were removed.
The validated report containing mapped entities is then used to automatically insert tagged values for the semantic concepts back into the XMI representation of the UML model.
After removing low quality reads and reads with 5′ primer contaminants, reads without 3′ primer, reads without the insert tag, reads with poly (A), and reads shorter than 18 nt, the clean reads were obtained.
The raw reads obtained from the Solexa sequencing were cleaned by removing adaptors, low quality tags as well as contaminant reads including those reads with 5´-primer contaminants, reads without 3´-primer, reads with poly A, reads without the insert tag, and reads with length less than 18 nt.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com