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?
Take a look here:
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.