Our lab had received RNAseq data from Illumina. I was able to do preliminary quality analysis using Fastqc app. Results are back however there seems to be something that I am not understanding.
All the sample have passed basic statistics and others except for 1) per base gc content 2)per base sequence content 3) sequence duplication levels.
I also checked the graphs and it looks like the first 10 reads on the fragments show high duplication levels and above mentioned problem. The end part of the fragments also show high duplication but not other two problems, which I think is due to poly A or 3' primer. But, statistics for over represented sequences has passed.
I also checked fragment reads in fastq files but it does show any of the adapter sequence in it.
So, my concerns are: 1) Could there be adapter/primer in my fragment? How do I check it? 2) If so how can I remove it: I need to prepare the adapter file. Is there some methods so I do it correctly with out removing the important part of my files.
Any help is appreciated.
Thanks,
Thanks,
All the sample have passed basic statistics and others except for 1) per base gc content 2)per base sequence content 3) sequence duplication levels.
I also checked the graphs and it looks like the first 10 reads on the fragments show high duplication levels and above mentioned problem. The end part of the fragments also show high duplication but not other two problems, which I think is due to poly A or 3' primer. But, statistics for over represented sequences has passed.
I also checked fragment reads in fastq files but it does show any of the adapter sequence in it.
So, my concerns are: 1) Could there be adapter/primer in my fragment? How do I check it? 2) If so how can I remove it: I need to prepare the adapter file. Is there some methods so I do it correctly with out removing the important part of my files.
Any help is appreciated.
Thanks,
Thanks,
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