Hello,
I am trying to align small/miRNAs to a fully assembled bacterial genome, and have been only getting 7% of reads to align. Of those 7%, almost all of them are only 10nt in length (or shorter). The size distribution has a peak around 30nt in length, and then slowly tails to 150. Most of the quality scores are 34 or higher.
Can anyone provide any suggestions? I have tried Bowtie2 default settings, local alignment, and endtoend with a 4nt seed. All have given me the same problem.
Thank you!
I am trying to align small/miRNAs to a fully assembled bacterial genome, and have been only getting 7% of reads to align. Of those 7%, almost all of them are only 10nt in length (or shorter). The size distribution has a peak around 30nt in length, and then slowly tails to 150. Most of the quality scores are 34 or higher.
Can anyone provide any suggestions? I have tried Bowtie2 default settings, local alignment, and endtoend with a 4nt seed. All have given me the same problem.
Thank you!
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