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Analysis of TraDIS data.

MD Matthew J. Dorman
TF Theresa Feltwell
DG David A. Goulding
JP Julian Parkhill
FS Francesca L. Short
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The analysis of TraDIS sequencing results was carried out using the Bio-TraDIS pipeline as described previously (43, 44), with minor modifications (see Text S1). All scripts used in this study are available at https://github.com/sanger-pathogens/Bio-Tradis and https://github.com/francesca-short/tradis_scripts. Comparisons between fractions were based on normalized read counts per gene. Genes with (i) reduced mutant abundance in the top fraction and (ii) increased mutant abundance in the middle or bottom fraction were called as decreased capsule hits, with thresholds of an absolute change in log2FC of >1 and a q value of <0.001. Increased capsule hits in NTUH-K2044 were defined as those with severely reduced mutant abundance in the middle fraction (log2FC < −3; q value < 0.001) without enrichment in the bottom fraction (log2FC < 1), with genes containing very few reads in any fraction excluded (i.e., the value corresponding to log2 counts per million in the top fraction was greater than 4).

Generation of the pan-genome and the method of enrichment analysis are described in Text S1.

Copyright and License information:  ©2018 Dorman 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.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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