2 comments on ““no @SQ lines in the header” and “missing header?”

  1. I had the same problem, using bowtie for mapping and the reason for the missing header was that bowtie has to be run with the -S option to produce SAM format.

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s