2015 OSU Workshop: Friday

• Created by Peter Hoyt, last modified about an hour ago

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ANNOUNCEMENTS:

1. Forms for students wanting to receive graduate student credit, by enrolling in BIOC 6820 this FALL (2016) are available from Dr. Peter Hoyt

2. IMMEDIATELY in the morning: Open your Discovery Environment and navigate to your MYDATA folder
   
   

   1. While in you MYDATA folder. Click on "Upload" and select "Import from URL"

   2. Paste in the following URLs to get these large datafiles into your MYDATA folder.
      
      

      http://de.iplantcollaborative.org/dl/d/4DF6947A-C2B3-423B-A08F-A17B9C75F1B0/846_large_blastx_out.txt

      http://de.iplantcollaborative.org/dl/d/885052A9-6CDB-4035-805E-4D4218E6648B/845_large_blastx_out.txt

SLIDES: https://drive.google.com/open?id=0BwLI3KMs2RkrVTI2Z2FGdEJkNU0

EXERCISES:  https://drive.google.com/open?id=1uPeBMNduOrQhJyUDDWXMmJUfek7uVsFzjAh2CmUUBcA

MEGAN5 Manual: http://ab.inf.uni-tuebingen.de/data/software/megan5/download/manual.pdf

iRODS-iDROPLinktosoftware: http://de.iplantcollaborative.org/dl/d/BB298AD6-3E1C-4004-A1B3-82705AD1D2C3/iDrop_windows-x64_2_0_1-beta3.exe

Group 1

454 vs Illumina
SRR1199563.sra  OSU  ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR119/SRR1199563/SRR1199563.sra
SRR1293629.sra  Illumina Interlaced ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR153/SRR1531023/SRR1531023.sra

(hint: de-interlace SRR1293629.sra to two fastq files)

Group 2
Metagenome analysis with MEGAN5
http://www.ncbi.nlm.nih.gov/sra/SRX266696%5Baccn%5D
http://www.ncbi.nlm.nih.gov/sra/SRX266695%5Baccn%5D

Group 3
https://pods.iplantcollaborative.org/wiki/display/eot/RNA-Seq_tutorial
/iplant/home/shared/iplant_training/intro_rna-seq/01_input_data
hy5_rep1.fastq
hy5_rep2.fastq
WT_rep1.fastq
WT_rep2.fastq

Group 4
Older sequence vs Newer sequence: Compare assemblies. Can you get N50? Other details?

 ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF_000347555.1_VHAOD131.1/GCF_000347555.1_VHAOD131.1_genomic.fna.gz
ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR925/SRR925383/SRR925383.sra

Group 5
454, MiSeq,  HiSeq
ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR120/SRR1207329/SRR1207329.sra
ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/ERR/ERR472/ERR472607/ERR472607.sra
ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/DRR/DRR015/DRR015701/DRR015701.sra