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Old 06-25-2010, 11:23 PM   #6
Nils Homer
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Location: Boston, MA, USA

Join Date: Nov 2008
Posts: 1,285

Originally Posted by jlfmssm View Post
but I got this:
[aimin@node01 all_sam_data]$ samtools view -S -X 1382_1.sam/1382_1.sam -o 1382_1_test.out
[samopen] no @SQ lines in the header.
[sam_read1] missing header? Abort!
What I should do now?
The lines "no @SQ lines in the header" and "missing header?" should tell you to check the header in the SAM file. Is there one? If not, you have to feed in your reference with the "-T" option.
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