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Kennedy-Lab-UW / Duplex-Sequencing

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The first tag was not being split correctly resulting in all unpaired #27

Closed nh13 closed 8 years ago

nh13 commented 8 years ago

reads.

@loeblab I think this is a fairly serious bug if I understand it correctly. Here are some SAM records on which to test. Prior to this fix, an unpaired consensus is made. After this fix, a proper double-strand consensus sequence is made.

TGGCGGGAAATGAACAAATCTCTT:1:4    99  1   115250972   255 108M    =   115251247   383 AATCAAATGTTTTAAACACTTTAGACCTCAGTACTTTCAGAAAGGGTGTCATATGGAAAATGTGCAGAAGAGGATAGGCAGAAACTCAAAAAACATATAGACAATAAC    JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ
AACAAATCTCTTTGGCGGGAAATG:2:3    163 1   115250972   255 108M    =   115251247   383 AATCAAATGTTTTAAACACTTTAGACCTCAGTACTTTCAGAAAGGGTGTCATATGGAAAATGTGCAGAAGAGGATAGGCAGAAACTCAAAAAACATATAGACAATAAC    JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ
TGGCGGGAAATGAACAAATCTCTT:2:4    147 1   115251247   255 108M    =   115250972   -383    ACCAGTGTGTAAAAAGCATCTTCAACACCCTATAAAAGGAAAAAATGAAAAAAAATGAGAGAGCTAGCTCAACGGACACAATCCAAATTATAAGCTCTCTTGCATTTG    JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ
AACAAATCTCTTTGGCGGGAAATG:1:3    83  1   115251247   255 108M    =   115250972   -383    ACCAGTGTGTAAAAAGCATCTTCAACACCCTATAAAAGGAAAAAATGAAAAAAAATGAGAGAGCTAGCTCAACGGACACAATCCAAATTATAAGCTCTCTTGCATTTG    JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ
nh13 commented 8 years ago

I think this also underscores the idea that we should not be modifying and parsing the read name, but instead using the SAM tags to store metadata about a read, as is the purpose of SAM tags.

scottrk commented 8 years ago

I'm open to doing this. What would you propose to put in as the read name? I'm open to suggestions.

On 4/13/16 12:38 PM, Nils Homer wrote:

I think this also underscores the idea that we should not be modifying and parsing the read name, but instead using the SAM tags to store metadata about a read, as is the purpose of SAM tags.

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