bowtie2 alignment with ambiguous bases

Question

[wizofe]

Hi all!

My reads contain several ambiguous (N) bases at both the 5'-end and 3'-end (specifically 5 and 4 bases respectively). So it looks like this:

$ head trimmed_Negative.fq  
@AFPN02.1_merge-1076320
NNNNNAAGGTCGCTAATCTCTTTACGCAGATTTTTTATTCCTTCAACTAACAGCGNNNN
+
#####BACCCGFGGGGGGGGGG1GGEGGG0GBGG1GGGGGGGG<GGGGGGGGBCG#### 
@AFPN02.1_merge-1076319
NNNNNCTTTATCCCGAAAGCGTTTGGTAGCTCGCTGGCATTAACGGGTTCGCCAGNNNN
+

Apart from trimming the ends in bowtie2 during a global alignment with a reference genome (using the -5 and -3 parameters) is there another suggested way to generate a reliable alignment using bowtie2?

I would prefer that instead of using another software :) Thanks for your help!

[GenoMax]

Those don't seem like ambiguous bases. That is no calls/bad data. If every read has these at the same positions then you should trim them off.