Real-Time PCR (qPCR) Pipeline

Auto-analysis for Real-Time PCR (qPCR) data.

This qPCR experiment usually have two group: Control (CK) and sample, and at least two type genes: Housekeeping Gene (HG) and Target Gene (TG). In our lab this usually label with ub7 and ve.

Congratulations! A alternative way to analysis of qPCR data can be find in : A shiny for analysis qRT-PCR data

• Dependencies
• INPUT
• USAGE
• OUTPUT

1. Dependencies

• python
  • collections
  • itertools
  • csv
  • pandas
  • numpy
  • sys
• R
  • ggplot2
  • gridExtra
  • ggthemes
  • ggsci
  • reshape2
  • dplyr

2. INPUT

There is a example input data in Example_data/.

3. USAGE

./qPCR.sh A B C D E F

Argument:

• A: absolute path of Input data (e, /public/home/hope/qPCR)
• B: Input Data (e, raw_input_qPCR.csv)
• C: Width of output pdf file
• D: Height of output pdf file
• E: Whether plot a scientific journals figure using the ggsci packages (yes or no)
• F: The sample name used as reference level in ANOVA analysis

Running on the example data:

./qPCR.sh /public/home/hope/qPCR raw_input_qPCR.csv 18 8 no CK

4. OUTPUT

• raw_input_qPCR_ubq7.csv
• raw_input_qPCR_ve.csv
• RQraw_input_qPCR_ve.csv
• RQraw_input_qPCR_ubq7.csv
• raw_input_qPCR_R.csv
• raw_input_qPCR_ANOVA.csv
• Pro_raw_input_qPCR_R.csv
• Pro_raw_input_qPCR.pdf
• raw_input_qPCR_T-test.pdf