FastQC analysis using Cyverse Discovery Environment
- synopsis
Asela Wijeratne<awijeratne@astate.edu>
rest
Data we are using for this analysis came from Loraine et al, 2015 study. In the original study, there are 10 samples (Five Controls and heat treated). Here we are using only 3 samples for each group (3 control and 3 heat treated). These files were downloaded from NCBI's Short Read Archive (SRA) using SRA toolkit.
First step of the data analysis is to check the quality of the sequences. For this purpose, we are using the FastQC tool on Cyverse DE.
First login to your Cyverse account using your name and password.
Then, go to your DE account.
- I have create public links for fastq files. Copy and paste URLs in the box (one for each box). You will need to do this for all 12 URLs. Then click on "Import from URL"
http://de.cyverse.org/dl/d/5B50EFE6-D0BA-4833-980E-E81E5B63C15E/Control1_1.fastq
http://de.cyverse.org/dl/d/BBFB60AC-8855-40AC-9634-7C62F5B9B02D/Control1_2.fastq
http://de.cyverse.org/dl/d/2AB5824F-73BA-4C6B-8530-457609F632BA/Control2_1.fastq
http://de.cyverse.org/dl/d/46E690E4-C4A0-495F-9B11-F12AD9A25EE3/Control2_2.fastq
http://de.cyverse.org/dl/d/7FEE6359-24AE-478D-A0B1-C6D2CA09E45E/Control3_1.fastq
http://de.cyverse.org/dl/d/8FBB264D-F0CA-4F2C-821A-DB1C709315B2/Control3_2.fastq
http://de.cyverse.org/dl/d/E7AD135C-F2BC-445C-BBC2-695B1D76B010/Heat1_1.fastq
http://de.cyverse.org/dl/d/46093383-493A-4D4E-A607-D3E56916DF59/Heat1_2.fastq
http://de.cyverse.org/dl/d/9668B243-7009-4AD3-BBDA-350D6A60119D/Heat2_1.fastq
http://de.cyverse.org/dl/d/FE1C3CC3-9133-4244-BCBB-816B8D2D5F97/Heat2_2.fastq
http://de.cyverse.org/dl/d/D635B6EE-BE26-4BC4-A058-3E51B1AA69C4/Heat3_1.fastq
http://de.cyverse.org/dl/d/F88561AF-CFF2-4FC8-B6B4-D8623779BB24/Heat3_2.fastq
Loraine AE, Blakley IC, Jagadeesan S, Harper J, Miller G, Firon N. Analysis and Visualization of RNA-Seq Expression Data Using RStudio, Bioconductor, and Integrated Genome Browser. Methods Mol Biol. 2015;1284:481-501. doi: 10.1007/978-1-4939-2444-8_24. PubMed PMID: 25757788.