diff --git a/MANUAL.markdown b/MANUAL.markdown index ca553832..b0596418 100644 --- a/MANUAL.markdown +++ b/MANUAL.markdown @@ -1827,13 +1827,15 @@ Spec][SAM]. Specify `--rg` multiple times to set multiple fields. See the --sam-omit-prim-seq + + When printing primary alignments, Bowtie 2 by default will write out the `SEQ` and `QUAL` strings. Specifying this option causes Bowtie 2 to print an asterisk in those fields instead. + - --omit-sec-seq