data_overview:2015:rna-seq
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data_overview:2015:rna-seq [2015/08/31 20:39] ceisenhart |
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 ====== | ||
| + | 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/ | | | ||
| - | |||
| - | ===== Files ===== | ||
| - | | File | Size | Reads| | ||
| - | |BS-AL-SmartSeq_S9_L005_R1_001.fastq.gz | 7.4G | | | ||
| - | |BS-AL-SmartSeq_S9_L005_R2_001.fastq.gz | 7.4G | | | ||
| - | |BS-AL-Tn5Prime_S7_L005_R1_001.fastq.gz | 1.1G | | | ||
| - | |BS-AL-Tn5Prime_S7_L005_R2_001.fastq.gz | 1.1G | | | ||
| - | |BS-PA-SmartSeq_S10_L005_R1_001.fastq.gz | 7.8G | | | ||
| - | |BS-PA-SmartSeq_S10_L005_R2_001.fastq.gz | 7.8G | | | ||
| - | |BS-PA-Tn5Prime_S6_L005_R1_001.fastq.gz | 2.2G | | | ||
| - | |BS-PA-Tn5Prime_S6_L005_R2_001.fastq.gz | 2.2G | | | ||
| - | |BS-P-SmartSeq_S11_L005_R1_001.fastq.gz | 6.5G | | | ||
| - | |BS-P-SmartSeq_S11_L005_R2_001.fastq.gz | 6.5G | | | ||
| - | |BS-P-Tn5Prime_S8_L005_R1_001.fastq.gz | 3.0G | | | ||
| - | |BS-P-Tn5Prime_S8_L005_R2_001.fastq.gz | 3.0G | | | ||
| Total = 56G Raw unprocessed data | Total = 56G Raw unprocessed data | ||
| ===== FastQC ===== | ===== FastQC ===== | ||
| - | The fastQC reports for the above files can be found online here [[http://hgwdev-ceisenhart.cse.ucsc.edu/~charles/BME235_backup/Data/2015/rnaSeq/fastQC/ | raw fastqc reports]]. | + | 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 ===== | ===== Processed data ===== | ||
| - | [[data_overview:2015:rna-seq:fastUniq | fastUniq ]] | ||
| - | [[data_overview:2015:rna-seq:fastUniq | fastUniq + 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. |
| + | |||
| + | |||
| + | [[http://hgwdev-ceisenhart.cse.ucsc.edu/~charles/BME235_backup/Data/2015/rnaSeq/fastUniq/fastqQuality | fastUniq + fastqQuality ]] fastqQuality removes low quality reads. | ||
| + | |||
| + | FastQC reports for the processed files can be found in the 'fastQC' subdirectories. | ||
| + | |||
| ===== 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.1441053560.txt.gz · Last modified: 2015/08/31 20:39 by ceisenhart
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