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Identification of small RNA clusters.

WK Wonyong Kim
CM Cristina Miguel-Rojas
JW Jie Wang
JT Jeffrey P. Townsend
FT Frances Trail
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The sRNA-seq and degradome-seq data were obtained from NCBI GEO (GSE87835) and NCBI SRA (PRJNA348145), respectively (47). In filamentous fungi, the size of a majority of sRNAs ranges from 17 to 27 nucleotides (nt), with a strong 5′ U preference (70 to 82%) (47, 118). Thus, clusters of 17- to 27-nt-long 5′-U sRNA reads were detected across the genome, using the ShortStack program (v3.8.2) (119) with the option arguments “--pad 22” and “--mincov 20.” Subsequently, the number of 5′ U sRNA reads aligned to different genomic features (e.g., coding regions) were counted for each sRNA cluster, using the htseq-count program (v0.8.0) (109). The degradome-seq data set was processed according to the previous study (47).

Copyright and License information:  ©2018 Kim et al.
This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.This content is distributed under the terms of the Creative Commons Attribution 4.0 International license.This content is distributed under the terms of the Creative Commons Attribution 4.0 International license.This content is distributed under the terms of the Creative Commons Attribution 4.0 International license.This content is distributed under the terms of the Creative Commons Attribution 4.0 International license.This content is distributed under the terms of the Creative Commons Attribution 4.0 International license.This content is distributed under the terms of the Creative Commons Attribution 4.0 International license.

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