From d2888c58139ff33ffac72fdc80c0c0972774f872 Mon Sep 17 00:00:00 2001
From: pdimens <pdimens@live.com>
Date: Thu, 12 Dec 2024 16:45:11 -0500
Subject: [PATCH] update text with terminal BX tag info

---
 harpy/downsample.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/harpy/downsample.py b/harpy/downsample.py
index a0c4bd5c..79a2a896 100644
--- a/harpy/downsample.py
+++ b/harpy/downsample.py
@@ -40,7 +40,9 @@ def downsample(input, invalid, output_dir, prefix, downsample, random_seed, setu
     Downsample data by barcode
 
     Downsamples FASTQ or BAM file(s) by barcode in the `BX` tag to keep all reads
-    from `-d` barcodes. Input can be:
+    from `-d` barcodes. The `BX:Z` tag must be the **last tag** in either the BAM
+    or FASTQ file(s). If the `BX` tag isn't terminal, use `bx_to_end.py` (provided
+    by Harpy) to move the tag to the end. Input can be:
     - one BAM file
     - two FASTQ files (R1 and R2 of a paired-end read set)