Update README.md

Author: jeremymiller

scripts/README.md

@@ -10,7 +10,7 @@ This document is divided into two sections based on which programming language w
 To replicate the figures in the paper, please use the code below:  
 
 1. **Code 1. Download and prepare the dissociation data** [(LINK TO SCRIPT)](http://htmlpreview.github.io/?https://github.com/AllenInstitute/patchseq_human_L23/blob/master/scripts/Code1_prepareComparisonDataSets.nb.html)  This script converts data downloaded from the [Allen Institute Cell Types Database](http://celltypes.brain-map.org/rnaseq) into a format compatible for use as comparison data to human and mouse Patch-seq.  
-2. **Code 2. Complete preparation for dissociation and Patch-seq data** [(LINK TO SCRIPT)](http://htmlpreview.github.io/?https://github.com/AllenInstitute/patchseq_human_L23/blob/master/scripts/Code2_prepare_data_L23exc.nb.html).  This script prepares the data for comparing mouse VISp and human MTG using dissociated and Patch-seq in superficial cortical layers, and outputs the results as R objects for remaining scripts.  
+2. **Code 2. Complete preparation for dissociation and Patch-seq data** [(LINK TO SCRIPT)](http://htmlpreview.github.io/?https://github.com/AllenInstitute/patchseq_human_L23/blob/master/scripts/Code2_prepare_data_L23exc.nb.html).  This script prepares the data for comparing mouse VISp and human MTG using dissociated and Patch-seq in superficial cortical layers, and outputs the results as R objects for remaining R scripts, **and outputs feather files for python scripts**.  
 3. **Code 3. Re-analysis and visualization of FACS data** [(LINK TO SCRIPT)](http://htmlpreview.github.io/?https://github.com/AllenInstitute/patchseq_human_L23/blob/master/scripts/Code3_FREM3_crossSpeciesComparisons.nb.html).  This script performs some statistical analyses and makes some UMAP plots showing glutamatergic neurons in supragranular layers of human MTG and mouse VISp for Figure 1.  One purpose is to quantify how cell type diversity, variation, and specialization of human types compares with mouse.  We also plot gene expression of some genes for Figure 6.  
 4. **Code 4. Visualization of mouse Patch-seq data** [(LINK TO SCRIPT)](http://htmlpreview.github.io/?https://github.com/AllenInstitute/patchseq_human_L23/blob/master/scripts/Code4_mouse_patchseq_visualization_L23exc.nb.html).  This script compares mouse FACs to Patch-seq data and visualizes the results for Figure 3.  It also outputs some plots and tables for later figures.  
 5. **Code 5. Mapping and visualization of human Patch-seq data** [(LINK TO SCRIPT)](http://htmlpreview.github.io/?https://github.com/AllenInstitute/patchseq_human_L23/blob/master/scripts/Code5_human_patchseq_mapping_L23exc.nb.html).  This script first performs Seurat mapping on the human Patch-seq cells (using FACS MTG data as references) and then compares and visualizes these results for Figure 3.  It also outputs some plots and tables (including mapping results) for later figures.