Wow! that's a clear explanation and I think I have a better understanding now thank you so much really!!!
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Understanding which Falco modules are important for assessing read quality
Hi everyone,
I’m an undergraduate student learning about NGS data analysis, and I’m trying to better understand how to interpret the different modules in Falco.
When performing quality control on sequencing reads, is it sufficient to primarily look at the Per Base Sequence Quality plot to assess whether the reads are of good quality, or is it important to examine all of the Falco modules?
I understand that the different modules are checking different aspects of the sequencing data, but I’m a little confused about how they complement each other and why there are so many separate plots. For example, what additional information do the other modules provide that would not be apparent from the Per Base Sequence Quality plot?
I would really appreciate an explanation of the reasoning behind checking the different modules and which ones are particularly important in different situations. I’m trying to understand the QC process conceptually rather than just following a checklist.
Thank you!
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1 answer
For example, what additional information do the other modules provide that would not be apparent from the Per Base Sequence Quality plot?
The best option is to look at the help documentation that is available here: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/ It goes over each module.
There are additional blog posts from authors of FastQC that can be found here: https://sequencing.qcfail.com/software/fastqc/
One thing to keep in mind is the kind of data you are analyzing (you have metagenomics as tag). Examples of "good" data in documentation are generally referring to common genomic sequence. If you have other types of data, then there may be some "fails" (red X) in FastQC module reports, that may not necessarily indicate bad data. It just shows the characteristics typical of that data (e.g. odd per sequence base plot with amplicons etc).
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It's essential to review most of the FastQC modules to ensure the data meets the expected quality parameters. Based on the visualisations in the report, you can decide on the trimming and filtering parameters.
A guide on how to read/interpret the results: https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/quality-control/tutorial.html
Thank you so much! I will definitely check out the material!