From c6db201b387030678f425f7d982a781c28d77fe7 Mon Sep 17 00:00:00 2001
From: James Webber <jamestwebber@users.noreply.github.com>
Date: Fri, 15 Nov 2024 08:54:25 -0500
Subject: [PATCH] Update README.md (#1245)

fixed documentation for paftools
---
 misc/README.md | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/misc/README.md b/misc/README.md
index 991f02c..f9d52f5 100644
--- a/misc/README.md
+++ b/misc/README.md
@@ -16,7 +16,8 @@ minimap2 -c test/MT-human.fa test/MT-orang.fa \
   | paftools.js liftover -l10000 - <(echo -e "MT_orang\t2000\t5000")     # liftOver
 # no test data for the following examples
 paftools.js junceval -e anno.gtf splice.sam > out.txt  # compare splice junctions to annotations
-paftools.js splice2bed anno.gtf > anno.bed             # convert GTF/GFF3 to BED12
+paftools.js splice2bed splice.sam > splice.bed             # convert PAF/SAM to BED12
+paftools.js gff2bed anno.gtf > anno.bed             # convert GTF/GFF3 to BED12
 ```
 
 ## Table of Contents