Source Code

Atlas Workflow Download

Filename Description
PerM Alignment tool to map the sequencing dataset to reference sequences
Sort_cut_split.sh Keep one map for one read, and then cut the valid columns and split the mapping results by chromosome
SplitFiles.py Python program called by Sort_cut_split.sh to split the mapping results by chromosome
qc Generate Quality Control report
   
pileUp.sh Convert the mapping results to wig and bed files
MergeExpression.sh Expression Level results by chromosome is merged to one file
JunctionExpressionLevelNRR_bowtie.py Count Splicing junction expression level with RPKM_RR method
GeneExpressionLevelNRR_bowtie.py Count Gene expression level with RPKM_RR method
ExonExpressionLevelNRR_bowtie.py Count Exon expression level with RPKM_RR method

DE Workflow Download

Filename Description
SampleCombine_WithReplicate.py Combine the gene expression level for different samples which will be output to Deseq_WithReplicate.r
Deseq_WithReplicate_FDR.r Differential expression analysis for conditions with replicate
SampleCombine_WithoutReplicate.py Combine the exon expression level for different samples which will be output to Deseq_WithoutReplicate.r
Deseq_WithoutReplicate_FDR.r Differential expression analysis for conditions without replicate

Rhesus Workflow Download

Filename Description
PerM Alignment tool to map the sequencing dataset to reference sequences
Sort_cut_split.sh Keep one map for one read, and then cut the valid columns and split the mapping results by chromosome
SplitFiles.py Python program called by Sort_cut_split.sh to split the mapping results by chromosome
MergeExpression.sh Expression Level results by chromosome is merged to one file
JunctionExpressionLevelNRR_bowtie.py Count Splicing junction expression level with RPKM_RR method
GeneExpressionLevelNRR_bowtie.py Count Gene expression level with RPKM_RR method
ExonExpressionLevelNRR_bowtie.py Count Exon expression level with RPKM_RR method

Pegasus
Download Pegasus WMS