Output & Temporary files¶
This page is intended for:
Developers: in order to make sure they have a consistent naming convention and can find each file easily
Users: in order to know what each output file represents
Through the pipeline, several temporary files will be generated, some of them are only used for settings and transitions, others for continuing the next step, the rest for publishing and interpreting a biological story.Below is three sections of tables for universal name rules.
Note
For data which has not been published on GEO use factor name plus your favorate number to replace the GSMID below.
Notation¶
Temporary files¶
| Name | Content | Tool used |
|---|---|---|
| ${DatasetID}_treat_rep${treat_rep}.sam | mapping result | External Tools |
| ${DatasetID}_control_rep${control_rep}.sam | mapping result | External Tools |
| ${DatasetID}.conf | configuration | Main program |
| ${DatasetID}_bedtools_dhs.txt | DHS peaks intersection | External Tools |
| ${DatasetID}_cor.R | correlation plot code | Buit-in tools |
| ${DatasetID}_seqpos.zip | Motif analysis | External Tools |
| ${DatasetID}_QC.tex | QC report code | pdftex |
| ${DatasetID}_mappable_ratio.pdf | Mapping QC result | R |
| ${DatasetID}_fastqc_score_distribution.pdf | Raw data QC | R |
| ${DatasetID}_peak_distribution.pdf | Peak calling QC | R |
| ${DatasetID}_velcro_ratio.pdf | Peak calling QC | R |
| ${DatasetID}_peak_overlap_DHS.pdf | Peak calling QC | R |
Output result¶
| Name | Content | Tool used |
|---|---|---|
| Folder | containing all results | Main Program |
| GSMIDlog | log | |
| GSMID_control_repnumber.bam | mapping result | External Tools |
| GSMID_treat_repnumber.bam | mapping result | |
| GSMID_repnumber_peaks.bed | Peak calling | MACS2 |
| GSMID_bedtools_dhs.txt | DHS peaks intersection | BEDtools |
| GSMID_cor.R | correlation plot code | Built-in tools |
| GSMID_seqpos.zip | Motif analysis | MDSeqpos |
| GSMID_QC.tex | QC report code | pdftex_ |
| GSMID_ceas.xls | CEAS | CEAS_ |
| GSMID_conserv.png | Phascon score plot | Built-in tools |
| GSMID_conserv.R | Phascon score | Built-in tools |
Final PDF Report¶
Provide the overall report of the whole pipeline for viewing general result.
| Name | Content | Tool used |
|---|---|---|
| GSMID_ceas_combined.pdf | Cistron annotation | CEAS |
| GSMID_QC.pdf | All quality control measurements | Main program |