Welcome to MTD: Microbial Transcriptome Database

Documentation: Scripts for Generating Circular Transcriptome Maps from RNAseq Data

Posted by: tsute on Mar 14, 2012 - 04:59 PM
DOC 


We provide two Perl scripts for drawing the circular profile map and comparative circular profile maps.


draw_circular_map_norm.pl

draw_circular_map_comp_norm.pl


Software requirement:


Perl (>=v5.8)

Perl modules:
Math::Trig
Number::Format

ImageMagick

Input data format:

1. Reference genome NCBI annotation files .ptt and .rnt

2. Mapped RNAseq reads

Your RNAseq reads need to be mapped to the reference genome and saved as the "pileup" format, with forward and reverse-complement data separated (two files).

Below are some test pileup files you can try o­n your computer:

A.fw.pileup
A.rc.pielup
B.fw.pileup
B.rc.pileup


For single RNAseq transcriptome profile, you need two pileup files (e.g., A.fw.pileup and A.rc.pileup, they are generated from samtools based o­n your fastq file) – o­ne for forward read counts, another reverse o­ne.

Then under Linux, run the included Perl script­:

 ./draw_circular_map_norm.pl A.fw.pileup A.rc.pileup > A.svg

convert A.svg A.png

 (convert is an ImageMagick command)

This will generate this image:



For comparing two transcriptome profiles you need 4 pileup files, each condition having both forward and reverse files.
And run this script­:

./draw_circular_map_comp_norm.pl A.fw.pileup A.rc.pileup B.fw.pileup B.rc.pileup > AB.svg

convert AB.svg AB.png

The AB.png looks like this:



Then you can view the png files using any graphic/image software.

If you run the scripts o­n your own data, remember to change some parameters in the beginning of each Perl script.


Please contact George Chen at tchen@forsyth.org if you have any question or require assistance.





 
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