GC-content – How to view this with TrueGC
January 16th, 2018
The intention of this post is to help you using our GC-content tool TrueGC which will give you information about the GC-content of the NGS sequences you have.
What you need to use TrueGC
To use TrueGC, you will need sequences. You can use those sequences which were directly given by the next generation sequencing machine or sequences processed by you. The format in which the sequences should be is fastq or fasta, not in the zipped file format “gz”. You should use not more than 10,000 sequences (this is enough to get an overview of the GC-content, and you will not waste time uploading your sequences). You can use any organism!
The input screen
Here you can see our input screen. We need you to provide the desired data for our statistics and your email address to send you a notification when the tool has finished the analysis or some error occurred.
You will get a pdf as result with several different pages:
GC-content per sequence
The first page gives you the GC-content in percent for every sequence you submitted. This is useful to get an idea of some sort of contamination with different GC-content sequences and easily spot which sequences are different, so you can take a closer look at them.
Histogram of GC-content
To give you a broader overview we have added a GC-content histogram, which should show you a distribution of GC-content counts around the expected GC-content of your genome or genome-part. In our example sequences it is a GC-content of 25%.
If you have any question about the science behind these tips, or any other question about contamination in sequencing, please contact us. If you have any other suggestions for blog post topics, please let us know.