4.0 years ago by
If you have the files in .fastq format you can use fastqc available from here: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Fastqc will work on zipped files, so you do not have to unzip them first. However, I think this format is what TGAC calls level 1 data. Level 3 data seems to me to be files in which the expression changes have already been calculated, so in other words much of the analysis has already been done. You would not be able to asses the quality of sequencing from this type of file. You would need the level 1 data (specifically, .fastq files.).
If you download fastqc and also the .fastq files, preferably zipped .fastq files, then you can just open the zipped .fastq files into fastqc. They will take a few minutes to load a single file. It will then provide a series of graphics. You can watch this 12 min. video made by the fastqc author on how to interpret the results here: https://www.youtube.com/watch?v=bz93ReOv87Y
(The names here can be a little confusing if you are beginning, so remember that .fastq is a sequencing file with results from the sequencing machine, and fastqc is a program you can download to assess the quality of the sequencing using the .fastq files.)