Disregard (not sure how to delete post)

DrD2009 · 08-07-2010, 12:08 PM

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.

ECO · 08-07-2010, 02:00 PM

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.

DrD2009 · 08-07-2010, 02:10 PM

Ah. You can keep it up if you think it will be beneficial to others.

ECO · 08-07-2010, 02:17 PM

Cool. Thanks for putting the title back!

DrD2009 · 08-07-2010, 02:18 PM

Not a problem.

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08-07-2010, 12:08 PM	#1
DrD2009 Member Location: Kansas City Join Date: Oct 2009 Posts: 88	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.

08-07-2010, 02:00 PM	#2
ECO --Site Admin-- Location: SF Bay Area, CA, USA Join Date: Oct 2007 Posts: 1,250	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.

08-07-2010, 02:10 PM	#3
DrD2009 Member Location: Kansas City Join Date: Oct 2009 Posts: 88	Ah. You can keep it up if you think it will be beneficial to others.

08-07-2010, 02:17 PM	#4
ECO --Site Admin-- Location: SF Bay Area, CA, USA Join Date: Oct 2007 Posts: 1,250	Cool. Thanks for putting the title back!

08-07-2010, 02:18 PM	#5
DrD2009 Member Location: Kansas City Join Date: Oct 2009 Posts: 88	Not a problem.