https://github.com/shengyongniu/bulk_ATAC_seq

This repo focus on bulk ATAC-seq analysis
https://github.com/shengyongniu/bulk_ATAC_seq

bulk-atac-seq

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This repo focus on bulk ATAC-seq analysis

• Host: GitHub
• URL: https://github.com/shengyongniu/bulk_ATAC_seq
• Owner: shengyongniu
• Created: 2017-11-03T11:48:49.000Z (about 7 years ago)
• Default Branch: master
• Last Pushed: 2018-09-15T02:39:45.000Z (over 6 years ago)
• Last Synced: 2024-02-12T23:46:05.368Z (10 months ago)
• Topics: bulk-atac-seq
• Language: Shell
• Size: 28.3 KB
• Stars: 2
• Watchers: 1
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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• awesome-atac-analysis - A bioinformatic analysis pipeline for bulk ATAC-seq

README

        
# 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