RNA-seq:
1)Demultiplexing
2)Quality control and reads trimming
3)Mapping and filtering
4)Estimating expression levels
5)Normalizing counts
6)Replicates evaluation
7)Differential expression analysis
Chip-seq:
1)Demultiplexing
2)Quality control and reads trimming
3)Mapping and filtering
4)Finding enriched regions
5)Differential binding analysis
6)Genetic annotations
Resequencing:
1)Demultiplexing
2)Quality control and reads trimming
3)Mapping and filtering
4)Coverage profile and variant calling
5)Merging results from all samples
6)Genomic annotations
7)Adding filtering flags
Exome sequencing:
1)Demultiplexing
2)Quality control and reads trimming
3)Mapping and filtering
4)Coverage profile and variant calling
5)Merging results from all samples
6)Genomic annotations
7)Marking known variants
8)Adding known variants