@@ -120,7 +120,7 @@ diffPeaks | *_diffbind.csv | Use only for replicated samples; CSV file of peaks
+ 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](https://hbctraining.github.io/Intro-to-ChIPseq/lessons/06_QC_cross_correlation.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 <1.1forinput.Column10(RSC)shouldbe> 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.
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@@ -128,6 +128,9 @@ diffPeaks | *_diffbind.csv | Use only for replicated samples; CSV file of peaks
## 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.txt). Please cite in publications: Pipeline was developed by BICF from funding provided by Cancer Prevention and Research Institute of Texas (RP150596). Also, please look out for our pipeline to be published in the future [HERE](https://zenodo.org/).
@@ -151,8 +154,5 @@ If you find an error, please let the [BICF](mailto:BICF@UTSouthwestern.edu) know
## 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/).
Please cite in publications: Pipeline was developed by BICF from funding provided by Cancer Prevention and Research Institute of Texas (RP150596).
## Citation
Please cite individual programs and versions used [HERE](docs/references.txt). Also, please look out for our pipeline to be published in the future [HERE](https://zenodo.org/).
@@ -23,7 +23,6 @@ Report issues to the Bioinformatic Core Facility [BICF](mailto:BICF@UTSouthweste
## Workflow Parameters
1. One or more input FASTQ files from a ChIP-seq expereiment and a design file with the link bewetwen the same file name and sample id (required) - Choose all ChIP-seq fastq files for analysis.
2. In single-end sequencing, the sequencer reads a fragment from only one end to the other, generating the sequence of base pairs. In paired-end reading it starts at one read, finishes this direction at the specified read length, and then starts another round of reading from the opposite end of the fragment. (Paired-end: True, Single-end: False) (required)
3. A design file listing sample id, fastq files, corresponding control id and additional information about the sample.
