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Sequence data processing

ES Elizabeth R. Sutton
YY Yachuan Yu
SS Sebastian M. Shimeld
HW Helen White-Cooper
aA and Luke Alphey
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The overall quality of the sequencing reads was assessed using FastQC (v0.10.1) [45]. Raw reads were processed to remove adapter sequence using FASTA/Q Clipper from the FASTX_Toolkit [46] and sequences of poor quality using Sickle [47]. Reference indexes of the Ae. aegypti genome assembly AaegL2 [48] (obtained from VectorBase) and the C. capitata genome assembly Ccap_1.0 [49] (obtained from NCBI) were constructed using Bowtie2 [50]. Trimmed reads were aligned to these indexes using TopHat2 (v2.0.9) [51]. Transcript assemblies were created from the alignments using the reference annotation based transcript assembly method [52] with Cufflinks (v2.1.1) [53] followed by Cuffmerge (v1.0.0) [54]. Transcript expression in each sample was quantified using Cuffdiff2 (v2.1.1) [55].

Copyright and License information: The Author(s). ©2016
Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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