Create README.md

Author: DivyanshiSrivastava

latent_embeddings/README.md

@@ -0,0 +1,35 @@
+### Bichrom Embeddings
+This module will report latent (2-D) co-ordinates for any DNA sequence and chromatin feature combination, given a trained Bichrom model.
+
+**(see trainNN README.md for details on how to train a Bichrom model)**
+
+### Usage
+
+To view help: ```python embed.py --help```
+```
+usage: embed.py [-h] -model MODEL -seq SEQ -chrom CHROM [CHROM ...] -length
+                LENGTH -outdir OUTDIR
+
+Derives and plots 2-D embeddings
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -model MODEL          Trained bichrom model
+  -seq SEQ              Sequence file, each line contains sequences associated
+                        with one genomic window
+  -chrom CHROM [CHROM ...]
+                        List of files, each containing chromatin features,
+                        associated with one genomic window per line
+  -length LENGTH        Length of training windows
+  -outdir OUTDIR        Output directory
+```
+
+### Input Data Requirements and Details
+
+* The **sequence file** contains: Sequences of length L. (Permitted bases: A, T, G, C, N)
+* The **chromatin files** contains: A binned vector of chromatin signal. 
+
+  (Example: If **L=500** and binsize **B=10**, then chromatin signal vector must contain **L/B** values)
+    
+  Note: Multiple chromatin track files can be provided with the -chrom argument (For example: ATAC-seq, H3K27ac, ... etc.).
+