README.md

bulk_ATAC_seq

A bioinformatic analysis pipeline for bulk ATAC-seq

1. FastQC

• Files: fastqc.sh
• Description:
  • This shell script help us understand the sequencing qualities of each samples and generate well-organized visualization of qualities

2. Trimming

• Files: trim.sh
• Description:
  • Check the fastqc result and decide how many bases to be trimmed

3. Mapping

• Files: mapping.sh, mapping.qsub
• Description:
  • Map reads and check reads size by the follwing script

4. Reads size check

• Files: flagstat.sh
• Description:
  • check the reads mapping size for experimental adjustment

5. Sort and remove duplicates

• Files: sam2Sortedbam_rmdup.qub, sam2Sortedbam_rmdup.sh
• Description:
• sort reads and remove duplicates. Note: Be careful for the memory issues. Need to check the result logs and set tmp dir in argument. Also,

6. Trim ChrY, ChrM, chrUn, and shift the coordinates

• Files: trim_Un_chY_chM_shift.qsub, trim_Un_chY_chM_shift.sh
• Description:
  • This file help trim the unused chromosome reads and shift the coordinates for the experimental reason of ATAC-seq

7. Delete negative reads

• Files: delete_negative.sh
• Description:
  • Delete the reads that are shifted to negative coordination

8. Convert BED file to BAM format for DiffBind

• Files: bedtobam.sh
• Description:
  • This script convert the BED format to BAM format for the following DiffBind analysis

9. Peaks calling

• Files: peakCalling_y.sh, peakCalling_y.qsub
• Description:
  • Call peaks by DiffBind

10. Filter out black list