DiffTF Documentation

diffTF Documentation

Release 1.0.0 Christian Arnold, Ivan Berest, Judith B. Zaugg

Aug 14, 2018

Quick Start and Installation

1 Try it out now!

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2 Prerequisites

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2.1 Snakemake . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

2.2 samtools, bedtools, Subread . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

2.3 R and R packages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

3 Run your own analysis

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4 Workflow

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5 Input

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5.1 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

5.2 General configuration file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

5.3 Input metadata . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20

6 Output

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6.1 FOLDER FINAL_OUTPUT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23

6.2 FOLDER PEAKS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25

6.3 FOLDER TF-SPECIFIC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26

6.4 FOLDER LOGS_AND_BENCHMARKS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28

6.5 FOLDER TEMP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28

7 Working with diffTF and FAQs

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7.1 General remarks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31

7.2 Executing diffTF - Running times and memory requirements . . . . . . . . . . . . . . . . . . . . . . 32

7.3 Running diffTF in a cluster environment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33

7.4 Frequently asked questions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33

8 Handling errors

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8.1 Error types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35

8.2 Identify the cause . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35

8.3 Common errors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37

8.4 Fixing the error . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37

9 Biological motivation

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10 Help, contribute and contact

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11 Citation

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12 Change log

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13 License

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diffTF Documentation, Release 1.0.0

Welcome to the diffTF documentation, and thank you for the interest in our software! These pages provide documentation and additional information for the diffTF pipeline. To get yourself oriented, check the menu on the left or search what you are looking for in the search field in the upper left corner. This site is organized into the following three parts:

Quick Start and Installation

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In order to avoid copyright disputes, this page is only a partial summary.

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