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Old 11-16-2012, 11:14 AM   #1
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Default Samtools: Paired reads with no Ref. name of the mate

In some bam files from paired reads data I see some of them with the field RNEXT or reference of the mate equal to "*". In these cases which flags should or not be used? Some examples of these reads are:

WESLEY:8:80:156:228/1/2        129     chr1    566704  255     69M     *       0       0       CCCTAATAATCGGTGCCCCCGATATGGCGTTTCCCCGCATAAACAACATAAGCTTCTGACTCTTACCCC   SWTTZ^WWYQYLQTQU^RRWZ`_ZROQ_^YYW^_aa_aa_`a^aaabaaababaaba`^``baa_bbbb
SOCAC:1:25:373:836/2/1  65      chr1    566430  255   4S54M18S        *       0       0       CTGTAGCCATTTTACCTCACCCCCACTGATGTTCGCCGACCGTTGACTAATCCCTACAGATCGGAAGAGCGTCGCG    abbabbbbbaaabbbababbaaabbaaZH[^]ab\aa]^aa\S_aaa\`Za`]_a`a^Ua_]LYL\MVXaYU^BBB
SOCAC:2:75:1643:1924/2/2        145     chr1    566428  255     63M6S   *       0       0       TCAGCCATTTTACCTCACCCCCACTGNTGTTCGCCGACCGTTGACTATTCTCCACAAACCACAGATCGG   a`bbaabababb`^baba`Wa`a[`^D\baa`\L\a_aZa_[``_`]a```]KYY]``WBBBBBBBBBB
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bam, flags, paired reads, sam, samtools

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