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Old 10-15-2011, 07:46 AM   #3
efoss
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Location: Seattle

Join Date: Jul 2011
Posts: 98
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Hi cedance,

I see output like this:


>CNAANATATATTGCACCATCCGCCGATCCGCAGGCAATTTTTAGGCCATT 0 unpaired <#0<#28899;<>><<?=<?>?@<==49=?;===?>1:;9:>>??;>??< HWI-ST156:39709NJACXX:8:1101:1790:1988

<ATCACAAACGAACACTTTAAAATCAGCTGTGATTTTGCTCGGGCTTCCTT 0 unpaired F?@@DFDDDDF;1C;BBDAEGCBFHJI<CGEIJEIEBF?D)6D@?FDHB= HWI-ST156:39709NJACXX:8:1101:1790:1988

>TNGANCTGGACCAGGTAATGGGATATACTGTTGTCCGGCGCCTGTTCAGC 0 unpaired 3#0:#2288>>?@@<@=??=<7:>9>>9@?@??>>9=88=?8?<1=???? HWI-ST156:39709NJACXX:8:1101:1980:1992

<AAAAACACTCACACCAAACATCAGCAGGATGCTGCAGCCCCCGGATGAGA 0 unpaired F<@<D+ADDDFF3??EDG?:CF?F<@;F811899?@C<@FG>AA'B;==E HWI-ST156:39709NJACXX:8:1101:1980:1992

>CTGANACTCGGGATCTGCACGGCGATAGCGGGCACCCAGGCTGGAGATGA 0 unpaired @?@F#2=BCDAA?FHIGCHIGIIIBEEGEHGGBACHEDFBCCCBABC>>> HWI-ST156:39709NJACXX:8:1101:1775:1997

This doesn't match the mandatory fields for a sam file:

http://samtools.sourceforge.net/SAM1.pdf

Thank you for the help.

Eric
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