User:Karmella Haynes/Notebook/PcTF Genomics/2014/04/02: Difference between revisions

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'''File Transfer Procedure'''
'''File Transfer Procedure'''
* Log-in to Saguaro via the Mac Terminal
* Log-in to Saguaro via the Mac Terminal
* Use the ssh file transfer protocol. Command: <br>saguaro1:~/ > scp file_to_transfer saguaro.fulton.asu.edu:/home/username/<br>file_to_transfer
* Use the ssh file transfer protocol. Command: <br>scp file_to_transfer user@remote_host:remote_file
 
** Need to finish: waiting to be granted scratch space from a2c2 **




Revision as of 17:33, 2 April 2014

Pc-TF Genomics <html><img src="/images/9/94/Report.png" border="0" /></html> Main project page
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04/02/14

  • STAR analysis of my ChIP-seq data


STAR analysis

  • Refer to 02/10/14 for the procedure and Command parameters
  • Refer to 12/19/11 for Hi-Seq parameters: fragment length (bioanalyzer result), read length
  • Input data must be a BED file
  • Example Command syntax: java -jar STAR.jar 100 1 true .5 10 true test_data1.txt false false test_out 1 true 10 5 0
Parameter Command 1
Extension length (frag - read) 100
Start coordinate 1
Right end inclusion true
FDR cut-off .5
Num perms 10
Remove identical reads true
sample file
    • Need to Finish **

Saguaro File Transfer

  • Last time, Mark Teng ran MACS on BAM files. I am concerned that some parameters might be incorrect. Also, since then, I generated input ChIP reads and would like to use this as input for MACS.
  • Jin Park offered to help re-run MACS peak finding again on BAM files
  • Must first upload BAM files to a2c2 to share with Jin.

File Transfer Procedure

  • Log-in to Saguaro via the Mac Terminal
  • Use the ssh file transfer protocol. Command:
    scp file_to_transfer user@remote_host:remote_file
    • Need to finish: waiting to be granted scratch space from a2c2 **




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