Hi all,
I'm newcomer to NGS field, and I would be grateful if someone could take a quick look at the FASTQC result of my NGS data (rice genome, 100 bp Paired-end, ~ 30x coverage) generated by Hiseq2000.
For the most part of the FASTQC result seem normal, except unnormal distribution for the per sequence GC content, the per base GC content, the sequence Duplication Levels and the Kmer Content.
Could this be due to PCR bias? Or be contaminated?
If conduct quality filtering with Fastx_toolkit, how do I set parameters?
Thanks a lot,
I'm newcomer to NGS field, and I would be grateful if someone could take a quick look at the FASTQC result of my NGS data (rice genome, 100 bp Paired-end, ~ 30x coverage) generated by Hiseq2000.
For the most part of the FASTQC result seem normal, except unnormal distribution for the per sequence GC content, the per base GC content, the sequence Duplication Levels and the Kmer Content.
Could this be due to PCR bias? Or be contaminated?
If conduct quality filtering with Fastx_toolkit, how do I set parameters?
Thanks a lot,
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