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Old 05-07-2012, 12:37 AM   #1
qwsqe
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Default CIGAR field of SAM file from Bowtie alignment

In a SAM file generated from Bowtie, I found one entry has '*' in the CIGAR field. What does this mean, bad alignment?

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Old 05-07-2012, 12:44 AM   #2
arvid
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It means "not available" in the SAM spec. Typically, this happens when the read isn't aligned (RNAME - 3rd field - is also '*' and 0x4 is set in the FLAG field).
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Old 05-07-2012, 05:31 AM   #3
qwsqe
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Thanks, arvid.
To what extend, Bowtie sets the FLAG to 0x4 for a read, and make the CIGAR field "not abailable". What are the measure and threshold bowtie uses for setting this?

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Old 05-07-2012, 05:39 AM   #4
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Well, using the settings (default or your specific choices), Bowtie found no reportable alignment for that read.
It is not possible to make a general statement about this behaviour here as it depends entirely on the settings you provided bowtie with and the nature of your reads and reference. Check the bowtie manual, typically you should look at alignment and reporting modes - these and their sub-options control alignment sensitivity and reporting filters.
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Old 05-08-2012, 05:28 AM   #5
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Hi Arvid,

Thank you very much for the help.
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