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Old 01-28-2013, 12:36 AM   #21
dpryan
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Quote:
Originally Posted by edge View Post
Hi Yuan,

Do you mind to explain what is the exact meaning of 0, 4, 16 if I map my single-end read against reference transcript by using bowtie?
As I know, 4 is refer to unmapped.
How about 0 and 16 represent?
Thanks.
See the SAM specification. In short 16 means the read was reverse complemented and 0 means none of the flags were set, so the read mapped to the forward strand.
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Old 01-28-2013, 12:51 AM   #22
edge
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Hi win804,

Many thanks for your advice.
I understand it now.
Thanks again.
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Old 01-28-2013, 12:55 AM   #23
edge
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Hi dpryan,

Many thanks for your reply.
I understand it right now
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Old 02-04-2013, 07:31 PM   #24
edge
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Hi win804,

Do you know what is the meaning of 20?
I run bwa to map my single-end read back to contig.
It shown 0, 4, 16, 20 in the sorted.bam T_T

Thanks for advice.
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Old 02-04-2013, 07:32 PM   #25
edge
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Hi dpryan,

Do you know what is the meaning of 20?
I run bwa to map my single-end read back to contig.
It shown 0, 4, 16, 20 in the sorted.bam T_T

Thanks for advice.
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Old 02-04-2013, 08:56 PM   #26
win804
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Hi Edge,
This page is probably useful for you: http://picard.sourceforge.net/explain-flags.html

20 means the read mapped in reverse strand and also the read is unmapped.
I know it's confusing. But the read is considered unmapped because it mapped to two different contigs (i.e. end of one contig and the start of another contig). You can check the read with the flag 20. It should be few bases from the end of the contig.

Thanks.
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