I am about to commit some serious time to analyzing data produced on a SOLiD 5500 and I had a few questions about sequence quality. First off, does quality matter that much if I have >10 million reads per sample? Second, does quality seriously alter mapping with TOPHAT (RNAseq analysis)? I would think this is less of a problem then if I was doing SNP detection or something. Finally, I can filter the reads with quality scores below 10 easily in GALAXY, but then I lose ~55% of the reads! Seems like a lot. Here are some images pre and post filtering. Am I just trying too hard to clean up the data or should I filter? Thanks in advance.
![](https://lh4.googleusercontent.com/Br-MDmaYaHSS4-V2BIr-CDvdQhKlyC4zvphRgD1uTws=w280-h207-p-no)
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The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...-
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