Originally posted by dnusol
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Maybe RNAseq is biased by nature?
Check these other threads
Application of sequencing to RNA analysis (RNA-Seq, whole transcriptome, SAGE, expression analysis, novel organism mining, splice variants)
Discussion of any scientific study related to high content or next generation genomics. Whole genome association, metagenomics, digital gene expression, etc.
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Originally posted by rhinoceros View PostLooks to me like the reads come from two very different sources (the two peaks). Perhaps even three sources.. I don't know. How are we supposed to tell since you didn't specify what was sequenced. Since the read counts (of the peaks) are somewhat similar, perhaps your source has two chromosomes, which have different GC (not unheard of).
The total RNA was extracted from one piece of mouse muscle by Qiagen RNeasy fibrous tissue mini kit. The quality of RNA were estimated by Agilent bioanalyzer. A260/A280 for all samples were around 2.0. RIN for all RNAs were around 10. It seems the quality of RNAs is excellent. And I didn't seem a chance to have other chromosomes.
The Libraries were prepared by a RNAseq center with an illumina TruSeq kit, but I know little about that...
Here is the whole FastQC report, which may give you more information. http://zgan.weebly.com/uploads/8/9/3...tqc_report.zip
More clues for me? ThanksLast edited by ZoeG; 06-18-2013, 03:53 PM.
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Originally posted by dnusol View Post
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Looks to me like the reads come from two very different sources (the two peaks). Perhaps even three sources.. I don't know. How are we supposed to tell since you didn't specify what was sequenced. Since the read counts (of the peaks) are somewhat similar, perhaps your source has two chromosomes, which have different GC (not unheard of).Last edited by rhinoceros; 06-14-2013, 04:23 AM.
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This link might be useful
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Contamination? What does this per sequence GC content mean?
Hello, I am quite new to RNAseq analysis.
When I did the quality control for my Illumina HiSeq data, I found an abnormal per sequence GC content, as the picture shows.
It seems some contamination?
Need help, thanksTags: None
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