WT: Added more info for input files

Author: williamthistle

vignettes/SPEEDI.Rmd

@@ -106,7 +106,7 @@ for folder in *_filtered_feature_bc_matrix; do
 done
 ```
 
-Within each folder, we have filtered data generated by Cell Ranger in the [MEX format](https://kb.10xgenomics.com/hc/en-us/articles/115000794686-How-is-the-MEX-format-used-for-the-gene-barcode-matrices). SPEEDI also works with [H5 format](https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/h5_matrices) files. If working with MEX files, sample data should always follow the standard naming convention (three files with names `barcodes.tsv.gz`, `features.tsv.gz`, and `matrix.mtx.gz`).
+Within each folder, we have filtered data generated by Cell Ranger in the [MEX format](https://kb.10xgenomics.com/hc/en-us/articles/115000794686-How-is-the-MEX-format-used-for-the-gene-barcode-matrices). SPEEDI also works with [H5 format](https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/h5_matrices) files. If working with MEX files, sample data should always follow the standard naming convention (three files with names `barcodes.tsv.gz`, `features.tsv.gz`, and `matrix.mtx.gz`). If working with H5 files, sample data file names should always end with `filtered_feature_bc_matrix.h5`. For example, `filtered_feature_bc_matrix.h5` and `Sample_1_filtered_feature_bc_matrix.h5` would both be fine, but `filtered_matrix.h5` would result in an error.
 
 **IMPORTANT**: SPEEDI expects data that have been [filtered](https://kb.10xgenomics.com/hc/en-us/articles/360001892491-What-is-the-difference-between-the-filtered-and-raw-gene-barcode-matrix-) using Cell Ranger or some other similar process.