From marshmallow version, developers need to ask for runtime permissions to user.
Let me give you whole process for asking runtime permissions.
I am using reference from here : marshmallow runtime permissions android.
First create a method which checks whether all permissions are given or not
private  boolean checkAndRequestPermissions() {
        int camerapermission = ContextCompat.checkSelfPermission(this, Manifest.permission.CAMERA);
        int writepermission = ContextCompat.checkSelfPermission(this, Manifest.permission.WRITE_EXTERNAL_STORAGE);
        int permissionLocation = ContextCompat.checkSelfPermission(this,Manifest.permission.ACCESS_FINE_LOCATION);
        int permissionRecordAudio = ContextCompat.checkSelfPermission(this, Manifest.permission.RECORD_AUDIO);
        List<String> listPermissionsNeeded = new ArrayList<>();
        if (camerapermission != PackageManager.PERMISSION_GRANTED) {
            listPermissionsNeeded.add(Manifest.permission.CAMERA);
        }
        if (writepermission != PackageManager.PERMISSION_GRANTED) {
            listPermissionsNeeded.add(Manifest.permission.WRITE_EXTERNAL_STORAGE);
        }
        if (permissionLocation != PackageManager.PERMISSION_GRANTED) {
            listPermissionsNeeded.add(Manifest.permission.ACCESS_FINE_LOCATION);
        }
        if (permissionRecordAudio != PackageManager.PERMISSION_GRANTED) {
            listPermissionsNeeded.add(Manifest.permission.RECORD_AUDIO);
        }
        if (!listPermissionsNeeded.isEmpty()) {
            ActivityCompat.requestPermissions(this, listPermissionsNeeded.toArray(new String[listPermissionsNeeded.size()]), REQUEST_ID_MULTIPLE_PERMISSIONS);
            return false;
        }
        return true;
    } 
Now here is the code which is run after above method. We will override onRequestPermissionsResult() method : 
 @Override
    public void onRequestPermissionsResult(int requestCode,
                                           String permissions[], int[] grantResults) {
        Log.d(TAG, "Permission callback called-------");
        switch (requestCode) {
            case REQUEST_ID_MULTIPLE_PERMISSIONS: {
                Map<String, Integer> perms = new HashMap<>();
                // Initialize the map with both permissions
                perms.put(Manifest.permission.CAMERA, PackageManager.PERMISSION_GRANTED);
                perms.put(Manifest.permission.WRITE_EXTERNAL_STORAGE, PackageManager.PERMISSION_GRANTED);
                perms.put(Manifest.permission.ACCESS_FINE_LOCATION, PackageManager.PERMISSION_GRANTED);
                perms.put(Manifest.permission.RECORD_AUDIO, PackageManager.PERMISSION_GRANTED);
                // Fill with actual results from user
                if (grantResults.length > 0) {
                    for (int i = 0; i < permissions.length; i++)
                        perms.put(permissions[i], grantResults[i]);
                    // Check for both permissions
                    if (perms.get(Manifest.permission.CAMERA) == PackageManager.PERMISSION_GRANTED
                            && perms.get(Manifest.permission.WRITE_EXTERNAL_STORAGE) == PackageManager.PERMISSION_GRANTED 
&& perms.get(Manifest.permission.ACCESS_FINE_LOCATION) == PackageManager.PERMISSION_GRANTED 
&& perms.get(Manifest.permission.RECORD_AUDIO) == PackageManager.PERMISSION_GRANTED) {
                        Log.d(TAG, "sms & location services permission granted");
                        // process the normal flow
                        Intent i = new Intent(MainActivity.this, WelcomeActivity.class);
                        startActivity(i);
                        finish();
                        //else any one or both the permissions are not granted
                    } else {
                        Log.d(TAG, "Some permissions are not granted ask again ");
                        //permission is denied (this is the first time, when "never ask again" is not checked) so ask again explaining the usage of permission
//                        // shouldShowRequestPermissionRationale will return true
                        //show the dialog or snackbar saying its necessary and try again otherwise proceed with setup.
                        if (ActivityCompat.shouldShowRequestPermissionRationale(this, Manifest.permission.CAMERA) 
|| ActivityCompat.shouldShowRequestPermissionRationale(this, Manifest.permission.WRITE_EXTERNAL_STORAGE) 
|| ActivityCompat.shouldShowRequestPermissionRationale(this, Manifest.permission.ACCESS_FINE_LOCATION)
 || ActivityCompat.shouldShowRequestPermissionRationale(this, Manifest.permission.RECORD_AUDIO)) {
                            showDialogOK("Service Permissions are required for this app",
                                    new DialogInterface.OnClickListener() {
                                        @Override
                                        public void onClick(DialogInterface dialog, int which) {
                                            switch (which) {
                                                case DialogInterface.BUTTON_POSITIVE:
                                                    checkAndRequestPermissions();
                                                    break;
                                                case DialogInterface.BUTTON_NEGATIVE:
                                                    // proceed with logic by disabling the related features or quit the app.
                                                    finish();
                                                    break;
                                            }
                                        }
                                    });
                        }
                        //permission is denied (and never ask again is  checked)
                        //shouldShowRequestPermissionRationale will return false
                        else {
                            explain("You need to give some mandatory permissions to continue. Do you want to go to app settings?");
                            //                            //proceed with logic by disabling the related features or quit the app.
                        }
                    }
                }
            }
        }
    }
If user clicks on Deny option then showDialogOK() method will be used to show dialog
If user clicks on Deny and also clicks a checkbox saying "never ask again", then explain() method will be used to show dialog. 
methods to show dialogs : 
 private void showDialogOK(String message, DialogInterface.OnClickListener okListener) {
        new AlertDialog.Builder(this)
                .setMessage(message)
                .setPositiveButton("OK", okListener)
                .setNegativeButton("Cancel", okListener)
                .create()
                .show();
    }
    private void explain(String msg){
        final android.support.v7.app.AlertDialog.Builder dialog = new android.support.v7.app.AlertDialog.Builder(this);
        dialog.setMessage(msg)
                .setPositiveButton("Yes", new DialogInterface.OnClickListener() {
                    @Override
                    public void onClick(DialogInterface paramDialogInterface, int paramInt) {
                        //  permissionsclass.requestPermission(type,code);
                        startActivity(new Intent(android.provider.Settings.ACTION_APPLICATION_DETAILS_SETTINGS, Uri.parse("package:com.exampledemo.parsaniahardik.marshmallowpermission")));
                    }
                })
                .setNegativeButton("Cancel", new DialogInterface.OnClickListener() {
                    @Override
                    public void onClick(DialogInterface paramDialogInterface, int paramInt) {
                        finish();
                    }
                });
        dialog.show();
    }
Above code snippet asks for four permissions at a time. You can also ask for any number of permissions in your any activity as per your requirements.