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data_overview:2015:rna-seq [2015/08/03 18:12] ceisenhart |
data_overview:2015:rna-seq [2015/08/31 20:48] ceisenhart Major changes... testing out a mix of wiki + good README's |
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====== Banana Slug RNA-Seq ====== | ====== Banana Slug RNA-Seq ====== | ||
- | ===== Files ===== | + | ===== Raw data ===== |
- | | File | Size | Reads| | + | The raw data can be accessed online [[http://genome-test.cse.ucsc.edu/~charles/BME235_backup/Data/2015/rnaSeq/ | here]]. |
- | | SW019_S1_L001_R1_001.fastq | 17G | 27,268,723 | | + | |
+ | Total = 56G Raw unprocessed data | ||
+ | |||
+ | ===== 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]]. | ||
+ | |||
+ | ===== Processed data ===== | ||
+ | FastQC reports for the processed files can be found through the ftp links below. | ||
+ | |||
+ | [[http://hgwdev-ceisenhart.cse.ucsc.edu/~charles/BME235_backup/Data/2015/rnaSeq/fastUniq/ | fastUniq]] fastUniq removed PCR duplicates. | ||
+ | |||
+ | |||
+ | [[http://hgwdev-ceisenhart.cse.ucsc.edu/~charles/BME235_backup/Data/2015/rnaSeq/fastUniq/fastqQuality | fastUniq + fastqQuality ]] fastqQuality removes low quality reads. | ||
- | Libraries are completed. Preliminary data is undergoing analysis. | ||
===== 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: |