- STAR analysis of my ChIP-seq data
- 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
|Extension length (frag - read)
|Right end inclusion
|Remove identical reads
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 firstname.lastname@example.org:/scratch/username
- 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_aln_sorted.bam (PcTF ChIP)
- 3_aln_sorted.bam (TF ChIP)
- 6_aln_sorted.bam (H3K27me3 ChIP)
- U2OSinput_sorted.bam (input)