User:Karmella Haynes/Notebook/PcTF Genomics/2014/04/02

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  • 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

  • 05/16/12 - 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.
  • Requested scratch space from Saguaro on 4/02/14

File Transfer Procedure (4/03/14)

  • Open the Mac Terminal. Do NOT log in to Saguaro.
  • Use the ssh file transfer protocol. Command:
    scp ~/Desktop/file_to_transfer
  • Enter the password to initiate the transfer
  • Open a new Terminal window, log in to Saguaro, "cd" into the scratch folder, and use the "dir" command to list the files

Files uploaded to Saguaro

  1. 1_aln_sorted.bam (PcTF ChIP)
  2. 3_aln_sorted.bam (TF ChIP)
  3. 6_aln_sorted.bam (H3K27me3 ChIP)
  4. U2OSinput_sorted.bam (input)