data_overview:2015:rna-seq
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data_overview:2015:rna-seq [2015/08/31 20:42] ceisenhart |
data_overview:2015:rna-seq [2015/09/02 16:11] ceisenhart Adding backlinks |
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| ====== Banana Slug RNA-Seq ====== | ====== Banana Slug RNA-Seq ====== | ||
| + | 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]]. | ||
| - | ===== Sequencing data ===== | ||
| - | | Library | Run | Location | Notes | | ||
| - | | - | - | http://genome-test.cse.ucsc.edu/~charles/BME235_backup/Data/2015/rnaSeq/ | | | ||
| Total = 56G Raw unprocessed data | Total = 56G Raw unprocessed data | ||
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| ===== Processed data ===== | ===== Processed data ===== | ||
| - | [[http://hgwdev-ceisenhart.cse.ucsc.edu/~charles/BME235_backup/Data/2015/rnaSeq/fastUniq/ | fastUniq]] | ||
| - | [[http://hgwdev-ceisenhart.cse.ucsc.edu/~charles/BME235_backup/Data/2015/rnaSeq/fastUniq/fastqQuality | fastqQuality ]] | ||
| - | Libraries are completed. Preliminary data is undergoing analysis. | + | [[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: | ||
data_overview/2015/rna-seq.txt · Last modified: 2015/09/02 16:12 by ceisenhart
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