This page is intended for:
Developers: in order to make sure they’re using the right format of data and right version of tool to test
Users: in order to know where they should go to download these data and tools
Data¶
Built-in Data¶
The Cpipe package includes all the build-in data for hg19 and mm9. For other species, you may need to download these data from data source or custom it yourself.
| Data Name | Used by | Data Source | Format |
|---|---|---|---|
| Chromesome length | samtools | UCSC table browser | 2-column |
| Chromesome length | CEAS | – | – |
| Genome backgroud annotation | CEAS | CEAS site | sqlite3 |
| DHS region | bedtools | Custom | BED |
| Velcro region | bedtools | Custom | BED |
| Motif database | MDSeqPos | MDSeqPos site | xml |
| FastQC result database | QCreport | Custom | bed |
| Data summary database | QCreport | Custom | bed |
External Data¶
Some data are too large to be included by the pipeline package, so you need to download these data from data source.
| Data Name | Used by | Data Source | Format |
|---|---|---|---|
| Bowtie pre-built index | Bowtie | Bowtie site | ebwt |
| Conservation profile | Conservation Plot | Cistrome site | Bigwig |
Tools¶
Built-in Tools¶
Built-in tools are the scripts that can be run from command-line independently when you have installed the Cpipe package.
| Tool Name | Modified from |
|---|---|
| Venn Diagram | |
| Conservation Plot | |
| Correlation plot | bigwig_correlation |
| bamtofastq | |
| wigTobigwiggle | |
| RegPotential | |
| sample_contamination |
External Tools¶
External Tools are the tools invoked by Cpipe by their path.
| Tool Name | Download source | Version |
|---|---|---|
| FastQC | ||
| R | ||
| Cython | ||
| MACS2 | MACS site | 2.0.10 20120605 |
| CEAS | CEAS site | 0.9.9.7 |
| bedtools | bedtools site | v2.16.2 |
| pybedtools | ||
| samtools | SAMtools site | 0.1.17 |
| Bowtie | Bowtie site | 0.12.8 |
| bedGraphToBigWig | UCSC utilities | v4 |
| FastQC | FastQC site | v0.10.1 |
| pdfTeX | pdfTex site | v1.40.10 |
| IGV |