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RNA-Seq data preprocessing

NO N. A. Omelyanchuk
DW D. S. Wiebe
DN D. D. Novikova
VL V. G. Levitsky
NK N. Klimova
VG V. Gorelova
CW C. Weinholdt
GV G. V. Vasiliev
EZ E. V. Zemlyanskaya
NK N. A. Kolchanov
AK A. V. Kochetov
IG I. Grosse
VM V. V. Mironova
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Raw reads were mapped onto the Arabidopsis genome (TAIR10) using SHRiMP (v2.2.3)27. Uniquely mapped reads were counted using the htseq-count program with the annotation file from TAIR1028. The DEGs were detected using the Bioconductor package DESeq29. As we investigated specificity in response to auxin, we filtered out the transcripts whose fold changes tended to zero or infinity. The genes were defined as DEGs if the Benjamini–Hochberg adjusted p-value was smaller than 0.05. Further functional annotation analysis was performed with 789 genes significantly upregulated and 659 genes downregulated by auxin.

Copyright and License information: The Author(s) ©2017
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