Ngs-Qc-Per Base Sequence Content Failed

Question

[williamjohn360]

I am newbie in NGS. We have sequenced non-model plant through illumina Hiseq 2000, and I have done the quality check for the raw sequence with fastqc, with fastqc quality check, the sequences passed all the test but failed in "Per Base Sequence Content". What should I do?. In what way I can improve the per base sequence content by quality filtering?. What type of quality filtering/tool should I use?

Answer 1

[Sean Davis]

Take a look here:

http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/4%20Per%20Base%20Sequence%20Content.html

FastQC is a great tool, but it has a set of expectations for what "good" data should look like. Your data may or may not meet those expectations, so there may not be a need to do anything.

In any case, I would highly suggest finding a local collaborator to work through your first dataset.

[Paul]

Yeah I absolutely agree with Sean. It very depends on your project - for example my data from HiSeq are very good, but fastqQC sometimes failed. Very important for checking all quality is to check PER BASE SEQUENCE CONTENT. So you probably dont have to worry about failed in "Per Base Sequence Content" if you passed in PER BASE SEQUENCE CONTENT.

[Dunois]

So you probably dont have to worry about failed in "Per Base Sequence Content" if you passed in PER BASE SEQUENCE CONTENT.

Erm what? This comment does not make any sense.