diff --git a/README.md b/README.md
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+++ b/README.md
@@ -5,6 +5,7 @@
[](https://www.nextflow.io/)
[](https://astrocyte-test.biohpc.swmed.edu/static/docs/index.html)
+[](https://doi.org/10.5281/zenodo.2648845)
## Introduction
diff --git a/docs/index.md b/docs/index.md
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-# Astrocyte ChIPseq analysis Workflow Package
+# BICF ChIP-seq Analysis Workflow
## Introduction
**ChIP-seq Analysis** is a bioinformatics best-practice analysis pipeline used for chromatin immunoprecipitation (ChIP-seq) data analysis.
@@ -7,16 +7,16 @@ The pipeline uses [Nextflow](https://www.nextflow.io), a bioinformatics workflow
### Pipeline Steps
-1) Trim adaptors TrimGalore!
-2) Align with BWA
-3) Filter reads with Sambamba S
-4) Quality control with DeepTools
-5) Calculate Cross-correlation using SPP and PhantomPeakQualTools
-6) Signal profiling using MACS2
-7) Call consenus peaks
-8) Annotate all peaks using ChipSeeker
-9) Use MEME-ChIP to find motifs in original peaks
-10) Find differential expressed peaks using DiffBind (If more than 1 experiment)
+ 1) Trim adaptors TrimGalore!
+ 2) Align with BWA
+ 3) Filter reads with Sambamba S
+ 4) Quality control with DeepTools
+ 5) Calculate Cross-correlation using SPP and PhantomPeakQualTools
+ 6) Signal profiling using MACS2
+ 7) Call consenus peaks
+ 8) Annotate all peaks using ChipSeeker
+ 9) Use MEME-ChIP to find motifs in original peaks
+ 10) Find differential expressed peaks using DiffBind (If more than 1 experiment)
## Workflow Parameters
@@ -25,41 +25,35 @@ The pipeline uses [Nextflow](https://www.nextflow.io), a bioinformatics workflow
pairedEnd - Choose True/False if data is paired-end
design - Choose the file with the experiment design information. TSV format
genome - Choose a genomic reference (genome).
+ skipDiff - Choose True/False if data if you want to run Differential Peaks
+ skipMotif - Choose True/False if data if you want to run Motif Calling
## Design file
- The following columns are necessary, must be named as in template. An design file template can be downloaded [HERE](https://git.biohpc.swmed.edu/bchen4/chipseq_analysis/raw/master/docs/design_example.csv)
-
- SampleID
- The id of the sample. This will be the header in output files, please make sure it is concise
- Tissue
- Tissue of the sample
- Factor
- Factor of the experiment
- Condition
- This is the group that will be used for pairwise differential expression analysis
- Replicate
- Replicate id
- Peaks
- The file name of the peak file for this sample
- bamReads
- The file name of the IP BAM for this sample
- bamControl
- The file name of the control BAM for this sample
- ContorlID
- The id of the control sample
- PeakCaller
- The peak caller used
-
+ The following columns are necessary, must be named as in template. An design file template can be downloaded [HERE](https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/blob/master/docs/design_example.txt)
+
+ sample_id
+ The id of the sample. This will be the name used in output files, please make sure it is concise and informative.
+ experiment_id
+ The id of the experiment. Used for grouping replicates.
+ biosample
+ The name of the biological sample.
+ factor
+ Factor of the experiment.
+ treatment
+ Treatment used in experiment.
+ replicate
+ Replicate number.
+ control_id
+ The sample_id of the control used for this sample.
+ fastq_read1
+ File name of fastq file, if paired-end this is read1.
+ fastq_read2
+ File name of read2 (for paired-end), not needed for single-end data.
### Credits
-This example worklow is derived from original scripts kindly contributed by the Bioinformatic Core Facility (BICF), Department of Bioinformatics
-
-### References
+This worklow is was developed jointly with the [Bioinformatic Core Facility (BICF), Department of Bioinformatics](http://www.utsouthwestern.edu/labs/bioinformatics/)
-* ChipSeeker: http://bioconductor.org/packages/release/bioc/html/ChIPseeker.html
-* DiffBind: http://bioconductor.org/packages/release/bioc/html/DiffBind.html
-* Deeptools: https://deeptools.github.io/
-* MEME-ChIP: http://meme-suite.org/doc/meme-chip.html
+Please cite in publications: Pipeline was developed by BICF from funding provided by **Cancer Prevention and Research Institute of Texas (RP150596)**.
diff --git a/docs/references.md b/docs/references.md
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@@ -50,3 +50,8 @@
16. **MultiQc**:
* Ewels P., Magnusson M., Lundin S. and Käller M. 2016. MultiQC: Summarize analysis results for multiple tools and samples in a single report. Bioinformatics 32(19): 3047–3048. doi:[10.1093/bioinformatics/btw354 ](https://dx.doi.org/10.1093/bioinformatics/btw354)
+
+17. **BICF ChIP-seq Analysis Workflow**:
+ * Venkat S. Malladi and Beibei Chen. (2019). BICF ChIP-seq Analysis Workflow (publish_1.0.0). Zenodo. doi:[10.5281/zenodo.2648845](https://doi.org/10.5281/zenodo.2648845)
+
+Please cite in publications: Pipeline was developed by BICF from funding provided by **Cancer Prevention and Research Institute of Texas (RP150596)**.