User:Karmella Haynes/Notebook/PcTF Genomics/2014/05/12

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  • Upload BAM files (again)

Saguaro File Transfer

  • Upload BAM files to scratch on Saguaro
  • Have to repeat this (from 04/02/14) because Natalia waited too long to process the files

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