export2sam.pl problem

novabc

Junior Member

Join Date: Dec 2010

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#1

export2sam.pl problem

12-06-2010, 06:22 AM

Hi:

I used export2sam.pl on export file created by CASAVA 1.7.0. However the generated sam file does not have @SQ lines, and had problem when used with samtools view etc.

export2sam.pl --read1=test_export.txt > test.sam
samtools view -h -S test.sam

Output is:
[samopen] no @SQ lines in the header.
[sam_read1] missing header? Abort!

Any suggestions? Thanks.

Jason
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maubp

Peter (Biopython etc)

Join Date: Jul 2009

Posts: 1544
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#2

12-06-2010, 08:58 AM

Does the samtools -t option to specify the reference FASTA file help?
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novabc

Junior Member

Join Date: Dec 2010

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#3

12-06-2010, 10:57 AM

Yes, adding -t option works. Thanks.
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