shengyongniu/bulk_rna_seq_tophat

A bioinformatic analysis pipeline for bulk RNA-seq

bulk_rna_seq_TopHat

A bioinformatic analysis pipeline for bulk RNA-seq

** Our approach refers to a Nature Protocol published in 2012 by Cole Trapnell et. al. **

1. Merge

• Files:
  • merge.sh
  • merge.qsub
• Description:
  • These two files are for merging bulk RNA-seq files from different experiments by multiple threads

2. FastQC

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

3. TopHat

• Files: tophat_mapping_y.sh and tophat_mapping_y.qsub
• Description:
  • These files utilize parallel computation to execute TopHat program. In this script, it will take UCSC hg 38 annotation file to conduct reads mapping with our RNA-seq fastq files.

4. Flagstat

• Files: RNA_flagstat.sh
• Description:
  • This step help us understand more accurate mapping qualities and percentage for double check

5. Cufflinks

• Files:
  • cufflinks_assemble.sh
  • cufflinks_assemble.qsub
• Description:
  • Assemble transcripts for each sample

6. Create assemblies.txt

• Description: Create a files called assemblies.txt that list the assembly files for samples.

7. CuffMerge

• Files: cuffmerge_y.sh
• Description:
  • Use Cuffmerge to run on all assemblies to create a single merged transcriptome annotation

8. CuffDiff

• Files:

  • B_cuffdiff.sh
  • CD4_cuffdiff.sh
  • CD8_cuffdiff.sh
  • M_cuffdiff.sh
  • cuffdiff_45hr.sh

• Description:

  • Run Cuffdiff by using the merged transcriptome assembly along with the BAM files from TopHat for each replicate in various samples

9. CummeRbund

• Files:
  • above CuffDiff.R scripts
• Description:
  • Use CummeRbund to understand differential expression genes