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Old 08-07-2010, 12:08 PM   #1
DrD2009
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Default Bowtie Strand Alignment

Nevermind. When I ran the alignments in Bowtie I forgot to remove the "-S" parameter.

*****************

I never really noticed this before, but Bowtie doesn't show - or + strand assignment. Instead it seems to give a code for what strand it aligns to in the second column of the output (SAM or Bowtie format).

The Bowtie manual says that the flag '16' represents the alignment to the reverse (-) reference strand. In my data I see '16', '0', '4' as alignment flags in the second column, '4' representing no alignment.

A flag '0' represents alignment to the forward (+) strand? Is that correct?

Just want to verify that.


Thanks.

Last edited by DrD2009; 08-07-2010 at 02:08 PM.
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Old 08-07-2010, 02:00 PM   #2
ECO
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You cant delete your own posts, but I will delete this one if you want. In the future, the community would benefit from leaving your thread/question intact, as someone else could certainly make the same mistake.
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Old 08-07-2010, 02:10 PM   #3
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Ah. You can keep it up if you think it will be beneficial to others.
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Old 08-07-2010, 02:17 PM   #4
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Cool. Thanks for putting the title back!
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Old 08-07-2010, 02:18 PM   #5
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Not a problem.
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