User:Karmella Haynes/Notebook/PcTF Genomics/2014/02/10: Difference between revisions

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PROCEDURE
PROCEDURE
* Download the zip file. Move unzipped '''STAR_1.0''' folder to Applications
* Download the zip file. Move unzipped '''STAR_1.0''' folder to Applications. STAR_1.0 folder contains:
* STAR_1.0 contents:
** README
** README
** STAR.jar
** STAR.jar
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| <right-end-inclusion infile> || ??? ||  
| <right-end-inclusion infile> || ??? ||  
|-
|-
| reagent 4 || #
| <FDR cutoff> ||??? ||  
|-
|-
| dH<sub>2</sub>O || #
| <numperms> || ??? ||
|-
|-
| &nbsp; || # μL
| &nbsp; || # μL

Revision as of 15:11, 10 February 2014

Pc-TF Genomics <html><img src="/images/9/94/Report.png" border="0" /></html> Main project page
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02/10/14

  • ChIP-seq analysis: STAR


ChIP-seq analysis via STAR

  • Significance Tester for the Accumulation of Reads (STAR) is a program used by Bramswig et al. (to determine enrichments of H3K27me3
  • Paper reference for STAR is Lefterova MI, et al. Cell-specific determinants of peroxisome proliferator-activated receptor gamma function in adipocytes and macrophages. Mol Cell Biol. 2010;30(9):2078–2089.
  • Website for STAR is http://www.cbil.upenn.edu/STAR/

PROCEDURE

  • Download the zip file. Move unzipped STAR_1.0 folder to Applications. STAR_1.0 folder contains:
    • README
    • STAR.jar
    • STAR.java
    • test_data.txt (Note: running the program with this file name gave an error. Changing the name to test_data1.txt fixes the problem)
  • Mac: Run the Terminal utility. COMMAND: open -a Terminal /applications/STAR_1.0
    • This opens a new Terminal window called STAR-1.0 -- bash -- [size of window]
  • README instructs user to try COMMAND: java -jar STAR.jar 10 1 true .5 10 true test_data1.txt false false test_out 1 true 10 5 0
  • Everything appears to be working


USAGE

  • The COMMAND java -jar STAR.jar 10 1 true .5 10 true test_data1.txt false false test_out 1 true 10 5 0 is a string of parameter values...
Parameter Description Example
<extension length> total fragment length minus the read length 10
<start coordinate infile> ??? 1
<right-end-inclusion infile> ???
<FDR cutoff> ???
<numperms> ???
  # μL

--> Reaction conditions



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