Astrocyte issueshttps://git.biohpc.swmed.edu/groups/BICF/Astrocyte/-/issues2020-04-30T16:16:25-05:00https://git.biohpc.swmed.edu/BICF/Astrocyte/sra_pipeline/-/issues/19Add concatination flag2020-04-30T16:16:25-05:00Jonathan GesellAdd concatination flagAdd a flag to concatenate the resulting fastq files if there are multiple files found (default is to concat).Add a flag to concatenate the resulting fastq files if there are multiple files found (default is to concat).Astrocyte FunctionalityJonathan GesellJonathan Gesellhttps://git.biohpc.swmed.edu/BICF/Astrocyte/sra_pipeline/-/issues/24Containerize Pipeline2020-06-17T16:37:54-05:00Jonathan GesellContainerize PipelineDesign the container so that it can be run by Docker as one image.Design the container so that it can be run by Docker as one image.Azure FunctionalityJonathan GesellJonathan Gesellhttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/91Update nf-tower token2021-07-25T17:02:51-05:00Venkat MalladiUpdate nf-tower token2.0.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/90Strip spaces in design file2020-12-29T17:26:45-06:00Venkat MalladiStrip spaces in design fileStrip leading or trailing spaces in design fileStrip leading or trailing spaces in design file2.0.0https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/89Diffbind is tsv not csv2020-12-29T17:23:49-06:00Venkat MalladiDiffbind is tsv not csvDiffbind output is actually tsv not csv file forat.Diffbind output is actually tsv not csv file forat.2.0.0https://git.biohpc.swmed.edu/BICF/Astrocyte/methylation_analysis/-/issues/5Add back tags per process2020-12-29T17:33:34-06:00Venkat MalladiAdd back tags per process1.0.0https://git.biohpc.swmed.edu/BICF/Astrocyte/methylation_analysis/-/issues/3Add a changelog2020-12-29T17:33:43-06:00Venkat MalladiAdd a changelog1.0.0https://git.biohpc.swmed.edu/BICF/Astrocyte/methylation_analysis/-/issues/2Update Readme2020-12-29T17:33:49-06:00Venkat MalladiUpdate ReadmeUpdate reamde to include and copy to docs
[![pipeline status](https://git.biohpc.swmed.edu/BICF/Astrocyte/methylation_analysis/badges/master/pipeline.svg)](https://git.biohpc.swmed.edu/BICF/Astrocyte/methylation_analysis/commits/master)...Update reamde to include and copy to docs
[![pipeline status](https://git.biohpc.swmed.edu/BICF/Astrocyte/methylation_analysis/badges/master/pipeline.svg)](https://git.biohpc.swmed.edu/BICF/Astrocyte/methylation_analysis/commits/master)
[![coverage report](https://git.biohpc.swmed.edu/BICF/Astrocyte/methylation_analysis/badges/master/coverage.svg)](https://git.biohpc.swmed.edu/BICF/Astrocyte/methylation_analysis/commits/master)|
[![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A50.31.0-brightgreen)](https://www.nextflow.io/)
[![Astrocyte](https://img.shields.io/badge/astrocyte-%E2%89%A50.3.1-blue)](https://astrocyte-test.biohpc.swmed.edu/static/docs/index.html)
[![DOI]()]()
Current version of the software and issue reports are at
https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis
To download the current version of the software
```bash
$ git clone git@git.biohpc.swmed.edu:BICF/Astrocyte/methylation_analysis.git
```
## Input files
##### 1) Fastq Files
+ You will need the full path to the files for the Bash Scipt
##### 2) Design File
+ The Design file is a tab-delimited file with 8 columns for Single-End and 9 columns for Paired-End. Letter, numbers, and underlines can be used in the names. However, the names can only begin with a letter. Columns must be as follows:
1. sample_id a short, unique, and concise name used to label output files; will be used as a control_id if it is the control sample
2. experiment_id biosample_treatment_factor; same name given for all replicates of treatment. Will be used for the consensus header.
3. biosample symbol for tissue type or cell line
4. factor symbol for antibody target
5. treatment symbol of treatment applied
6. replicate a number, usually from 1-3 (i.e. 1)
7. control_id sample_id name that is the control for this sample
8. fastq_read1 name of fastq file 1 for SE or PC data
9. fastq_read2 name of fastq file 2 for PE data
+ See [HERE](test_data/test_design_pe.txt) for an example design file, paired-end
+ See [HERE](test_data/test_design_se.txt) for an example design file, single-end
##### 3) Bash Script
+ You will need to create a bash script to run the Methylation pipeline on [BioHPC](https://portal.biohpc.swmed.edu/content/)
+ This pipeline has been optimized for the correct partition
+ See [HERE](docs/Methylation.sh) for an example bash script
+ The parameters that must be specified are:
## Pipeline (Details output and steps)
+
Add flowchart
See [FLOWCHART](docs/flowchart.pdf)
## Output Files
Folder | File | Description
--- | --- | ---
d
## Common Quality Control Metrics
+ These are the list of files that should be reviewed before continuing on with the CHIPseq experiment. If your experiment fails any of these metrics, you should pause and re-evaluate whether the data should remain in the study.
1. multiqcReport/multiqc_report.html: follow the ChiP-seq standards [HERE](https://www.encodeproject.org/chip-seq/);
2. experimentQC/*_fingerprint.pdf: make sure the plots information is correct for your antibody/input. See [HERE](https://deeptools.readthedocs.io/en/develop/content/tools/plotFingerprint.html) for more details.
3. crossReads/*cc.plot.pdf: make sure your sample data has the correct signal intensity and location. See [HERE](hhttps://ccg.epfl.ch//var/sib_april15/cases/landt12/strand_correlation.html) for more details.
4. crossReads/*.cc.qc: Column 9 (NSC) should be > 1.1 for experiment and < 1.1 for input. Column 10 (RSC) should be > 0.8 for experiment and < 0.8 for input. See [HERE](https://genome.ucsc.edu/encode/qualityMetrics.html) for more details.
5. experimentQC/coverage.pdf, experimentQC/heatmeap_SpearmanCorr.pdf, experimentQC/heatmeap_PearsonCorr.pdf: See [HERE](https://deeptools.readthedocs.io/en/develop/content/list_of_tools.html) for more details.
## Common Errors
If you find an error, please let the [BICF](mailto:BICF@UTSouthwestern.edu) know and we will add it here.
## Citation
Please cite individual programs and versions used [HERE](docs/references.md), and the pipeline doi:[](). Please cite in publications: Pipeline was developed by BICF from funding provided by Cancer Prevention and Research Institute of Texas (RP150596).
## Programs and Versions
## Credits
This example worklow is derived from original scripts kindly contributed by the Bioinformatic Core Facility ([BICF](https://www.utsouthwestern.edu/labs/bioinformatics/)), in the [Department of Bioinformatics](https://www.utsouthwestern.edu/departments/bioinformatics/).1.0.0Spencer BarnesSpencer Barneshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/41Update multiqc version/references report2020-07-01T14:36:11-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduUpdate multiqc version/references report* Add astrocyte version to version report (if param.astrocyte=true)
* Add astrocyte reference to reference report (if param.astrocyte=true)* Add astrocyte version to version report (if param.astrocyte=true)
* Add astrocyte reference to reference report (if param.astrocyte=true)Version 2.1.0https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/85Update multiqc version/references report2020-06-23T15:48:58-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduUpdate multiqc version/references report* Add astrocyte version to version report (if param.astrocyte=true)
* Add astrocyte reference to reference report (if param.astrocyte=true)* Add astrocyte version to version report (if param.astrocyte=true)
* Add astrocyte reference to reference report (if param.astrocyte=true)2.0.0https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/83Unique Experiment check2020-06-23T15:49:10-05:00Venkat MalladiUnique Experiment checkCheck design file for unique experiments and replicates before starting.Check design file for unique experiments and replicates before starting.2.0.0https://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/36update version of nextflow2020-06-23T16:02:27-05:00Holly Ruessupdate version of nextflowupdate nextflow/0.31.0 to nextflow/19.09.0update nextflow/0.31.0 to nextflow/19.09.0Version 2.1.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/74Annotepeaks2020-06-23T15:49:23-05:00Venkat MalladiAnnotepeaksSeperate annotate peaks with different design file reading to chunk processing so it doesn't read it into memory.Seperate annotate peaks with different design file reading to chunk processing so it doesn't read it into memory.2.0.0https://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/35Change to 256 only if job fails2020-06-23T16:02:34-05:00Holly RuessChange to 256 only if job failsMay need to incorporate maxErrors and maxRetries into processesMay need to incorporate maxErrors and maxRetries into processesVersion 2.1.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/34Diff Peak analysis2020-06-23T16:02:40-05:00Holly RuessDiff Peak analysisVersion 2.1.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/33Motif search in peaks2020-06-23T16:02:46-05:00Holly RuessMotif search in peaksVersion 2.1.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/70Use specific meme file in motif search2020-12-29T17:30:57-06:00Holly RuessUse specific meme file in motif searchDownload meme files from http://meme-suite.org/doc/download.html Motif DB
Add into biohpc config file the correct meme file for each species
Change the meme chip scriptDownload meme files from http://meme-suite.org/doc/download.html Motif DB
Add into biohpc config file the correct meme file for each species
Change the meme chip script2.0.0https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/69add checks to determine if fastq files are in proper format and not truncated2020-06-23T15:52:26-05:00Spencer Barnesadd checks to determine if fastq files are in proper format and not truncatedWe can maybe implement this tool:
https://genome.sph.umich.edu/wiki/FastQValidatorWe can maybe implement this tool:
https://genome.sph.umich.edu/wiki/FastQValidator2.0.0https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/63Annotate Diffbind output2020-12-29T17:27:14-06:00Holly RuessAnnotate Diffbind outputAnnotate the output of diffBind
use the same annotations as with peak annotations
See Holly for updates on how to use gencode.gtf fileAnnotate the output of diffBind
use the same annotations as with peak annotations
See Holly for updates on how to use gencode.gtf file2.0.0Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/62Filter reads increase memory2020-12-29T17:30:29-06:00Venkat MalladiFilter reads increase memoryIncrease memory allocation upon failure:
https://github.com/nf-core/chipseq/blob/master/conf/base.config
https://www.nextflow.io/docs/latest/process.html?highlight=retryIncrease memory allocation upon failure:
https://github.com/nf-core/chipseq/blob/master/conf/base.config
https://www.nextflow.io/docs/latest/process.html?highlight=retry2.0.0Jeremy MathewsJeremy Mathews