---
name: "saint-spc-ctrl"
section: "1"
platform: "linux"
package: "saint"
version: "2.5.0+dfsg-4+b3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/saint-spc-ctrl"
---

# saint-spc-ctrl(1)

run SAINT with control data

## NAME

saint-spc-ctrl - run SAINT with control data

## SYNOPSIS

**saint-spc-ctrl** *\[interactionFile\] \[preyFile\] \[baitFile\] \[nburnin\] \[niter\] \[lowMode\] \[minFold\] \[normalize\]*

## DESCRIPTION

-

  nburnin = 2000: number of burn-in iterations in MCMC.

-

  niter = 10000: number of main iterations in MCMC.

-

  lowMode = 0/1 : exclude extremely high counts in the model.

-

  \- If baits are densely connected or dataset is small (few baits), use 1.

-

  \- otherwise, use 0.

-

  minFold = 0/1 : forcing separation between true and false distributions.

-

  \- If user wishes to allow typical contaminants with significant

-

  differential enrichment over control purifications, use 0.

-

  \- otherwise, use 1.

-

  normalize = 0/1 : divide the counts by the total spectral counts in each IP.

-

  nburnin = 2000: number of burn-in iterations in MCMC.

-

  niter = 10000: number of main iterations in MCMC.

-

  lowMode = 0/1 : exclude extremely high counts in the model.

-

  \- If baits are densely connected or dataset is small (few baits), use 1.

-

  \- otherwise, use 0.

-

  minFold = 0/1 : forcing separation between true and false distributions.

-

  \- If user wishes to allow typical contaminants with significant

-

  differential enrichment over control purifications, use 0.

-

  \- otherwise, use 1.

-

  normalize = 0/1 : divide the counts by the total spectral counts in each IP.

## SEE ALSO

You can download a PDF file with more detailed instructions from

-

  http://sourceforge.net/projects/saint-apms/files/

which is called saint-vignette-\<YYYYMonDD\>.pdf.