To begin, download the compressed analysis pipeline from GitHub by typing the command in the terminal. After downloading, enter the command to decompress the zip file. Once the decompression is complete, remove the zip file and change the decompressed folder name.
Then, set executable permissions for all the shell scripts in the working directory. From the available options, locate the appropriate installation shell script. Look for a script named Script_01_Installation.sh.
Open the terminal and type echo SHELL to check the default shell used in the active terminal. If bash is not the default shell, set it by typing chsh s in the terminal. Type the fast queue download script in the terminal, or drag the script file into the terminal and press enter.
After running the script, check the log file for error messages. Now, enter the trimming script in the terminal and execute it. Next, type the bowtie2 index creation script in the terminal and execute it.
Finally, run the bowtie2 mapping script and press enter. Type the bam filtering and sorting script in the terminal and execute it. Next, convert bam to BEDPE, BED, and bedGraph formats by typing the appropriate command in the terminal and pressing enter.
Perform normalization using the SRPMC method, then run the insert size analysis script. Perform peak calling using the MACS command in the terminal. Afterward, type the command for peak calling using SEACR and press enter.
Create peak BED files by using the appropriate command in the terminal, and then filter the peaks. Next, enter the command to merge MACS peaks. Type the command in the terminal to merge SEACR peaks.
Generate a correlation plot, and run the command for principle component analysis in the terminal. Then, create a Venn diagram comparing different methods using the appropriate command. Enter the command to generate a Venn diagram for replicates.
Finally, generate a focused peak center heat map. Then, generate a whole peak center heat map.
