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