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