Merge pull request #630 from CGATOxford/ts_add_option_to_extract_from…

…_read2_only adds option to extract barcode from read2 only
CGATOxford · Mar 13, 2024 · 156e285 · 156e285
2 parents cac1f00 + c229bd9
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diff --git a/doc/faq.md b/doc/faq.md
@@ -58,3 +58,8 @@
 - **Can I use whitelist without UMIs?**
 
 	Strickly speaking, yes, but only with `--extract-method string`. If you use `--extract-method regex` and don't provide both a UMI and Cell barcode position in the regex, you'll get an error.
+
+&nbsp;
+- **Can I extract barcodes from just read2?**
+
+    Yes, you can use --read2-only with `umi_tools extract` & `whitelist`. Previously, we had been recommending users achieve this by simply swapping the read1 and read2 input files around. That's still a viable approach. 
diff --git a/tests/extract_help b/tests/extract_help
@@ -69,6 +69,7 @@ Options:
     --3prime            barcode is on 3' end of read.
     --read2-in=READ2_IN
                         file name for read pairs
+    --read2-only        Only extract from read2
     --filtered-out=FILTERED_OUT
                         Write out reads not matching regex pattern to this
                         file