Readme For Study GSE58455, GSE56890 Prep

9/14/2014

By: Calvin D. Cox

Clemson University 2014

Summary: This is an NGS Workflow that I constructed to evaluate expression levels in select genes from Mouse Samples.

Methods For GSE58455:

**All procedures listed take place in /feltus/calvinc/USCMouse1_58455/ unless specified otherwise in code or comments.

1. Downloaded Accession Data from NCBI Database Experiment URL: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE58455
2. Input *.sra into Fastq Dump
3. Input SRR1391033.sra into fastqc for a base comparison post-trim
4. Input *.fastq into Trimmomatic (v .30)
5. Input SRR1391033.sra into fastqc for post-trim analysis
6. Run *.fastq through Tophat (v?)
7. Ran treatment .bam outputs through cuffdiff (Cufflinks v 2.1.1)
8. Extracted relevant gene data.

Treatment Key

Embryo 13.5 Week

SRR1391033.sra
SRR1391036.sra
SRR1391034.sra
SRR1391038.sra
SRR1391039.sra
SRR1391035.sra
SRR1391037.sra

16 Week Adult

SRR1391051.sra
SRR1391050.sra
SRR1391049.sra
SRR1391048.sra
SRR1391047.sra
SRR1391046.sra

Sham 12 Week Adult

SRR1391052.sra
SRR1391053.sra
SRR1391054.sra
SRR1391055.sra

6 Week Adult

SRR1391040.sra
SRR1391041.sra
SRR1391042.sra
SRR1391043.sra
SRR1391044.sra
SRR1391045.sra

Files were stored in tophat (/feltus/calvinc/USCMouse1_58455/tophat) used the script below to move them to bambin and rename them with unique names. ** for i in SRR*trimTop; do cp /common1/feltus/calvinc/USCMouse1_58455/tophat/$i/accepted_hits.bam ../$i.accepted_hits.bam; done **

Bam Output with Matching Treatments

(Directory: /common1/feltus/calvinc/Mouse_Study_First/trimbin/bambin)

E13.5 SRR33trimTop.accepted_hits.bam SRR34trimTop.accepted_hits.bam SRR35trimTop.accepted_hits.bam SRR36trimTop.accepted_hits.bam SRR37trimTop.accepted_hits.bam SRR38trimTop.accepted_hits.bam SRR39trimTop.accepted_hits.bam

16 wk SRR46trimTop.accepted_hits.bam SRR47trimTop.accepted_hits.bam SRR48trimTop.accepted_hits.bam SRR49trimTop.accepted_hits.bam SRR50trimTop.accepted_hits.bam SRR51trimTop.accepted_hits.bam

Sham_12wk SRR52trimTop.accepted_hits.bam SRR53trimTop.accepted_hits.bam SRR54trimTop.accepted_hits.bam SRR55trimTop.accepted_hits.bam

Adult 6wk SRR40trimTop.accepted_hits.bam SRR41trimTop.accepted_hits.bam SRR42trimTop.accepted_hits.bam SRR43trimTop.accepted_hits.bam SRR44trimTop.accepted_hits.bam SRR45trimTop.accepted_hits.bam