A issue in NGS data 1/assignment 4

[Jiawen-Liu]

FastQC is used for quality control for fastq file. In assignment 4, the FastQC report for SRR5882792_10M_1.fastq/SRR5882792_10M_2.fastq. fail to show the quality of genome and adaptor type.

[kortschak]

/cc @steveped

[smped]

Hi @Jiawen-Liu,

Thanks for letting us know. I'm a little unclear as to your question though. A FastQC report with no adapter detected can mean that there are no adapters present, or that an unknown adapter type was used. Which do you suspect it is?

Also, a FastQC report can only report on the reads with a library, not on genome quality. Assuming you meant the former, can you advise on which plots you were able to see in your report? Is this the plot with Per Base Quality Scores that's missing?

[Jiawen-Liu]

Hi, @steveped
Actually, there is no adapter shown in FastQC. But I searched this genome in NCBI and Illumina and I found that there is adapter for this genome. Therefore, I am not sure whether there is adapter.
In addition, I see the plot with per base quality scores that's missing.
Thank you