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Old 02-04-2009, 08:10 AM   #1
Aengus
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Location: london

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Default SOAP output format - description?

Hi,

I have searched the SOAP website and read the paper but I cant find a description for all the columns in the ouput.

Col1 = Read Seq_ID
Col2 = Read Sequence
Col3 = Read Sequence Quality
Col4 = ? I have the digit 1 here
Col5 = ? I have the letter 'a' here
Col6 = Read Length
Col7 = Strand
Col8 = Reference Seq_ID
Col9 = Position of start of read alignment
Col10= 0/1/2 - I think this is the number of mismatches?
Col11= base change - cant work out this out eg G->10C7


Can anyone fill in the blanks for me?

Regards
Aengus
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Old 02-04-2009, 11:34 AM   #2
swbarnes2
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column 4 is uniqueness.

if you gave it paired end data, a and b signify the two halves of the same paried end read. With single end data, its always a.

Yes, column 10 is the number of mismatches. The base change the reference letter and its position, and the read's letter and its quality score. The output is a littel trickier with indels.
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Old 09-08-2010, 06:26 AM   #3
AXW
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I realize this is an old thread, but I had trouble finding the specifics as well. Ended up going to the SOAPv1 page, found the output file description there.

http://soap.genomics.org.cn/soap1/#Formatofoutput
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