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data_overview:2015:rna-seq [2015/07/16 18:50] ceisenhart created |
data_overview:2015:rna-seq [2015/09/02 16:12] (current) ceisenhart [Banana Slug RNA-Seq] |
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====== Banana Slug RNA-Seq ====== | ====== Banana Slug RNA-Seq ====== | ||
- | Libraries are completed. Preliminary data is undergoing analysis. | + | To see how we are using this data, please view [[https://banana-slug.soe.ucsc.edu/post-assembly_analysis:2015:rna_scaffolding | this page]]. |
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+ | ===== Raw data ===== | ||
+ | The raw data can be accessed online [[http://genome-test.cse.ucsc.edu/~charles/BME235_backup/Data/2015/rnaSeq/ | here]]. | ||
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+ | Total = 56G Raw unprocessed data | ||
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+ | ===== FastQC ===== | ||
+ | The fastQC reports for the raw files can be found online here [[http://hgwdev-ceisenhart.cse.ucsc.edu/~charles/BME235_backup/Data/2015/rnaSeq/fastQC/ | raw fastqc reports]]. | ||
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+ | ===== Processed data ===== | ||
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+ | [[http://hgwdev-ceisenhart.cse.ucsc.edu/~charles/BME235_backup/Data/2015/rnaSeq/fastUniq/ | fastUniq]] fastUniq removes PCR duplicates. | ||
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+ | [[http://hgwdev-ceisenhart.cse.ucsc.edu/~charles/BME235_backup/Data/2015/rnaSeq/fastUniq/fastqQuality | fastUniq + fastqQuality ]] fastqQuality removes low quality reads. | ||
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+ | FastQC reports for the processed files can be found in the 'fastQC' subdirectories. | ||
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===== RNA Extraction ===== | ===== RNA Extraction ===== | ||
RNA was extracted from three tissues, the albumen, proximal albumen and penis. The protocol used for RNA extraction is as follows: | RNA was extracted from three tissues, the albumen, proximal albumen and penis. The protocol used for RNA extraction is as follows: |