Converts NGS data to TilingScan format.
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README.md
cover2tiling.cpp

README.md

Release notes 0.1

cover2tiling

Cover2Tiling converts NGS data (from a sorted BAM file) into TilingScan input format.

Requirements:

Compilation

Linux

First you must download and install the C++ compiler. You can do this opening a new terminal and executing:

sudo apt-get install g++

Now, 'cd' to the cover2tiling directory containing the source and type

g++ cover2tiling.cpp -o cover2tiling 

This will generate an executable for cover2tiling. Now copy this file to your data directory, or add it to your PATH.

Windows

You can compile cover2tiling using an IDE, such as DevC++.

How to use

First, you must generate the coverage from your BAM file with the data (note that your BAM must be sorted). For this, open a new terminal and 'cd' to your data directory. Next, use the SAMTOOLS mpileup command to get the coverage from your BAM file:

samtools mpileup your_bam_file.bam > cover.txt

Remember to replace your_bam_file.bam with the name of your real BAM file. This will generate you a file named cover.txt with the coverage. Now, use the cover2tiling to generate the TilingScan format from the cover file:

cover2tiling cover.txt output.txt N

Where:

  • cover.txt is the output file of samtools mpileup comand.
  • output.txt is the output file to be used in TilingScan.
  • N is the average nucleotides for each hit. It must be odd.

That's all! Now you can use the output file generated in TilingScan.

Get help

If you have any question, or want a personalized version of cover2tiling, feel free to contact with us:

V.Arnau: Vicente.Arnau@uv.es J.M.Juanes: J.Miguel.Juanes@uv.es