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--- data_overview:2015:rna-seq [2015/08/03 18:12]
ceisenhart
+++ data_overview:2015:rna-seq [2015/09/02 16:12] (current)
ceisenhart [Banana Slug RNA-Seq]
@@ Line 1: / Line 1: @@
 ====== 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]].
-===== 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 =====
+[[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.
-Libraries are completed. Preliminary data is undergoing analysis.
 ===== RNA Extraction =====
 RNA was extracted from three tissues, the albumen, proximal albumen and penis. The protocol used for RNA extraction is as follows:

Banana Slug Genomics