# Contents
`ChIP-TRA1-snakefile` - Snakemake-based workflow to identify TRA-1 binding sites from raw ChIP-seq files.  

`smallRNA-SNPC13-DE.Rmd` - differential expression analysis using as input the gene expression matrix generated from the ***small-RNA-SNPC13-snakefile*** workflow.  

`smallRNA-SNPC13-snakefile` - Snakemake-based workflow to generate a gene expression matrix from raw small RNA-seq fastq data. Execute using ***submit-smallRNA-SNPC13-snakefile.sh***.  

`run-ChIP-TRA1-snakefile.sh` - batch input file to submit ***ChIP-TRA1-snakefile*** as a batch job.  

`run-smallRNA-SNPC13-snakefile.sh` - batch input file to submit ***smallRNA-SNPC13-snakefile*** as a batch job.  


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## Resources
The small RNA-seq and ChIP-seq data have been deposited in NCBI under GEO accession number: GSE152831.

[bbmap 38.23](http://jgi.doe.gov/data-and-tools/bb-tools/)  
[ENCODE ce11 blacklist](https://github.com/Boyle-Lab/Blacklist/)  
[FastQC 0.11.7](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)  
[Picard 2.22.1](http://broadinstitute.github.io/picard/)  
[Trim Galore! 0.5.0](http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/)  

<br>

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