Hello everybody,
I have to map small reads (15 to 29 nt ) on transcripts in order to find gene that are targetted by a small class of ncRNA. nothing in known about this targetting, but i need to put a seed length of 16nt with no mismatches.
Attached is a picture showing the kind of targetting we are searching for.
I run bowtie with the following option :
, but no alignement is returned.
I would like to know if an option exist to tell bowtie that only the seed is take into account during the mapping, not the remaining sequence ...
Thanks in advance for your help.
I have to map small reads (15 to 29 nt ) on transcripts in order to find gene that are targetted by a small class of ncRNA. nothing in known about this targetting, but i need to put a seed length of 16nt with no mismatches.
Attached is a picture showing the kind of targetting we are searching for.
I run bowtie with the following option :
Code:
bowtie -l 16 -n 0 -v 3 --nofw -t transcript_clip -c AATTGAATAAATATATGTCAG
I would like to know if an option exist to tell bowtie that only the seed is take into account during the mapping, not the remaining sequence ...
Thanks in advance for your help.
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