diff --git a/src/main.rs b/src/main.rs
index 106e4eb..1b480ce 100644
--- a/src/main.rs
+++ b/src/main.rs
@@ -36,11 +36,11 @@ enum Commands {
             .args(&["rows", "cols"]),
     ))]
     Subset {
-        /// Input MTX file
-        #[arg(short, long)]
-        input: String,
+        /// Input MTX file or directory containing matrix.mtx.gz, features.tsv.gz, and barcodes.tsv
+        #[arg(short = 'i', long = "input")]
+        input: Option<String>,
 
-        /// Output MTX file
+        /// Output MTX file or directory name (if directory is used, matrix.mtx.gz, features.tsv.gz, and barcodes.tsv will be subsetted)
         #[arg(short, long)]
         output: String,
 
@@ -72,7 +72,14 @@ fn main() -> Result<(), Box<dyn Error>> {
             cols,
             no_reindex,
         } => {
-            subset::subset_matrix(&input, &output, rows, cols, no_reindex)?;
+
+            subset::subset_matrix(
+                input,
+                &output,
+                rows,
+                cols,
+                no_reindex,
+            )?;
         }
     }
 
diff --git a/src/subset.rs b/src/subset.rs
index fd08d76..468b36f 100644
--- a/src/subset.rs
+++ b/src/subset.rs
@@ -2,19 +2,25 @@ use crate::io_utils;
 use std::collections::{HashMap, HashSet};
 use std::error::Error;
 use std::io::{self, BufRead, Write};
+use std::path::Path;
+use std::fs;
 
 pub fn subset_matrix(
-    input_file: &str,
-    output_file: &str,
+    input: Option<String>,
+    output: &str,
     rows_file: Option<String>,
     cols_file: Option<String>,
     no_reindex: bool,
 ) -> Result<(), Box<dyn Error>> {
+
     // Check if both rows_file and cols_file are None
     if rows_file.is_none() && cols_file.is_none() {
         return Err("At least one of --rows or --cols must be specified.".into());
     }
 
+    // check if input is a file or directory
+    let is_directory = input.as_ref().map_or(false, |path| Path::new(path).is_dir());
+
     // Read the indices to retain
     let rows_to_retain = if let Some(ref file_path) = rows_file {
         read_indices(file_path)?
@@ -41,17 +47,80 @@ pub fn subset_matrix(
     };
 
     let rows_set: HashSet<usize> = if !rows_to_retain.is_empty() {
-        rows_to_retain.into_iter().collect()
+        rows_to_retain.clone().into_iter().collect()
     } else {
         HashSet::new() // Empty set indicates all rows are retained
     };
 
     let cols_set: HashSet<usize> = if !cols_to_retain.is_empty() {
-        cols_to_retain.into_iter().collect()
+        cols_to_retain.clone().into_iter().collect()
     } else {
         HashSet::new() // Empty set indicates all columns are retained
     };
 
+    if is_directory {
+        fs::create_dir_all(output)?;
+        let dir_path = Path::new(input.as_ref().unwrap());
+        let output_path = Path::new(output);
+        let matrix_file = dir_path.join("matrix.mtx.gz").to_string_lossy().into_owned();
+        let output_matrix = output_path.join("matrix.mtx").to_string_lossy().into_owned();
+        let features_file = dir_path.join("features.tsv.gz").to_string_lossy().into_owned();
+        let barcodes_file = if dir_path.join("barcodes.tsv.gz").exists() {
+            dir_path.join("barcodes.tsv.gz").to_string_lossy().into_owned()
+        } else {
+            dir_path.join("barcodes.tsv").to_string_lossy().into_owned()
+        };
+
+        let output_features = output_path.join("features.tsv").to_string_lossy().into_owned();
+        let output_barcodes = output_path.join("barcodes.tsv").to_string_lossy().into_owned();
+
+        subset_mtx_file(&matrix_file, &output_matrix, &row_mapping, &col_mapping, &rows_set, &cols_set)?;
+        subset_dimnames_file(&features_file, &output_features, &rows_to_retain, &row_mapping)?;
+        subset_dimnames_file(&barcodes_file, &output_barcodes, &cols_to_retain, &col_mapping)?;
+
+    } else {
+        let matrix_file = input.as_ref().unwrap();
+        subset_mtx_file(&matrix_file, output, &row_mapping, &col_mapping, &rows_set, &cols_set)?;
+    }
+
+    Ok(())
+}
+
+fn read_indices(file_path: &str) -> Result<Vec<usize>, Box<dyn Error>> {
+    let reader = io_utils::get_reader(file_path)?;
+    let mut indices = Vec::new();
+
+    for (line_number, line) in reader.lines().enumerate() {
+        let line = line?;
+        let trimmed_line = line.trim();
+
+        if trimmed_line.is_empty() {
+            continue;
+        }
+
+        match trimmed_line.parse::<usize>() {
+            Ok(idx) => indices.push(idx),
+            Err(_) => {
+                eprintln!(
+                    "Warning: Failed to parse index on line {} in '{}'",
+                    line_number + 1,
+                    file_path
+                );
+            }
+        }
+    }
+
+    Ok(indices)
+}
+
+fn subset_mtx_file(
+    input_file: &str,
+    output_file: &str,
+    row_mapping: &Option<HashMap<usize, usize>>,
+    col_mapping: &Option<HashMap<usize, usize>>,
+    rows_set: &HashSet<usize>,
+    cols_set: &HashSet<usize>,
+) -> Result<(), Box<dyn Error>> {
     let temp_data_file = "temp_data.mtx";
 
     // Open the input and temporary data files
@@ -140,9 +209,11 @@ pub fn subset_matrix(
     // Now write the header to the output file
     let mut output_writer = io_utils::get_writer(output_file)?;
 
-    // Write the header lines
-    for line in &header_lines {
-        writeln!(output_writer, "{}", line.trim_end())?;
+    // Write the header lines excluding the last one
+    for (index, line) in header_lines.iter().enumerate() {
+        if index < header_lines.len() - 1 {
+            writeln!(output_writer, "{}", line.trim_end())?;
+        }
     }
 
     // Calculate new dimensions
@@ -180,31 +251,32 @@ pub fn subset_matrix(
     Ok(())
 }
 
-fn read_indices(file_path: &str) -> Result<Vec<usize>, Box<dyn Error>> {
-    let reader = io_utils::get_reader(file_path)?;
-    let mut indices = Vec::new();
 
-    for (line_number, line) in reader.lines().enumerate() {
-        let line = line?;
-        let trimmed_line = line.trim();
+fn subset_dimnames_file(
+    input_file: &str,
+    output_file: &str,
+    indices_to_retain: &[usize],
+    mapping: &Option<HashMap<usize, usize>>,
+) -> Result<(), Box<dyn Error>> {
+    let reader = io_utils::get_reader(input_file)?;
+    let mut writer = io_utils::get_writer(output_file)?;
 
-        if trimmed_line.is_empty() {
-            continue;
-        }
+    let indices_set: HashSet<usize> = indices_to_retain.iter().cloned().collect();
 
-        match trimmed_line.parse::<usize>() {
-            Ok(idx) => indices.push(idx),
-            Err(_) => {
-                eprintln!(
-                    "Warning: Failed to parse index on line {} in '{}'",
-                    line_number + 1,
-                    file_path
-                );
-            }
+    for (index, line) in reader.lines().enumerate() {
+        let line = line?;
+        if indices_set.is_empty() || indices_set.contains(&(index + 1)) {
+            let _ = if let Some(ref mapping) = mapping {
+                *mapping.get(&(index + 1)).unwrap_or(&(index + 1))
+            } else {
+                index + 1
+            };
+            writeln!(writer, "{}", line)?;
         }
     }
 
-    Ok(indices)
+    writer.flush()?;
+    Ok(())
 }
 
 fn create_index_mapping(indices: &[usize]) -> HashMap<usize, usize> {