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Normalized Stochasticity Ratio (NST)

IEG-SAP Tutorial. Normalized Stochasticity Ratio (NST). Daliang Ning 2019.6.16. Login. http://ieg3.rccc.ou.edu:8080/. This is still a beta version of our newest statistical analysis pipeline. Contact Daliang to set up your account. Change password. User  Preferences  Change password.

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Normalized Stochasticity Ratio (NST)

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  1. IEG-SAP Tutorial Normalized Stochasticity Ratio(NST) Daliang Ning 2019.6.16

  2. Login • http://ieg3.rccc.ou.edu:8080/ This is still a beta version of our newest statistical analysis pipeline. Contact Daliang to set up your account

  3. Change password • User  Preferences  Change password 1 2 3

  4. Create new history • “History” is like a “folder” under your account. 1 3 2

  5. Upload OTU table (1) • OTU table should be a tab-delimited txt file. • first column should be OTU IDs, first row should be sample IDs

  6. Upload OTU table (2) • Get Data  Upload File  Choose local file then select your OTU table file 1 5 2 4 3

  7. Upload treatment information • Treatment information table should be a tab-delimited txt file. • First column should be sample IDs • Upload useGet Data  Upload File  Choose local file

  8. Upload tree file (if calculate phylogenetic NST) • The phylogenetic tree file should be .nwk format • Uploading is the same as uploading OTU table.

  9. Reduce taxa number (1) • The computation (especially phylogenetic NST) can take days or even weeks for a large dataset with too many taxa. • Thus, a feasible practice is to reduce the taxa number (better around 10,000). Or split the OTU table to smaller ones by dividing samples into groups, each group represents a regional pools. • The pipeline has a tool to reduce taxa number by removing relatively rare OTUs. • However, it is still not explicitly investigated how the NST result will be affected by reducing taxa number.

  10. Reduce taxa number (2) • Get data  Reduce Taxa 1 3 2 Use lower value if you need 4 5 Better <1% of the target taxa number. 6 Do not use Rarefy. The other two methods are preferred, although we provide three options for people to try. 7

  11. Match IDs • Check whether the OTU IDs in OTU table and tree file match well. 3. You may use the OTU after reducing the taxa number if necessary. 1 3 4 2 5 6 7 8 9

  12. Calculate phylogenetic distance matrix (if calculate phylogenetic NST) • Diversity  Big Phylogenetic Distance 3 1 4 5 2 6

  13. Taxonomic NST 3 1 • Mechanism  Taxonomic NST 4* 2 Only for GeoChip data 5 6 7 8 9 Up to 8 parallel threads 10 13 11 12 Description of indexes in output files

  14. Phylogenetic NST 3 • Mechanism Big Phylogenetic NST 1 4 5 6 7 8 2 9 Up to 8 parallel threads 10 11 13 12

  15. Download results • The result files are tab-delimited txt files • You may download themand use excel to open them 1 3 2 4

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