Hello,

I haven't worked with miRNA mapping..( the specie is mouse) It is the first time to do it.

I have read a lot of posting and web-site to map my microRNA data.

Here is what I follow.

**1) trim the adapter using cutadapt**

When I looked at my fastq file (single-end), read length was 36 bp.. by inspecting the eye-ball test, I could not find my common sequences. (So, I am not sure my fastq file has been already trimmed or not . So I kept both versions... )This is my command... (comes from http://www.ark-genomics.org/events-online-training-eu-training-course/adapter-and-quality-trimming-illumina-data)

```
cutadapt -a CGACAGGTTCAGAGTTCTACAGTCCGACGATC \
         -a TACAGTCCGACGATC \
         -a ATCTCGTATGCCGTCTTCTGCTTG \
         -e 0.1 -O 5 -m 15 \
         -o xxx_microRNA_adaprm.fastq xxx_microRNA.fastq
```

So, I have 2 version fastq files. (`xxx_microRNA.fastq`, `xxx_microRNA_adaprm.fastq`)

**2) Local bowtie2 alignment of miRNA data**

(I generated the reference with bowtie-build directly from the hairpin FASTA file downloaded from miRBase.)

```
Bowtie2-build hairpin_mms.fa hairpin_mms.fa
Bowtie2-build mature_mms.fa mature_mms.fa
Bowtie2 -local -N 1 -L 16 -x hairpin_mms.fa -U fastq/xxx_microRNA(_adaprm).fastq -S xxxx.sam
```

The bowtie2 mapping returns the following result.. (for both versions)

I should have done something wrong...

```
2849144 reads; of these:
  2849144 (100.00%) were unpaired; of these:
    2847350 (99.94%) aligned 0 times
    933 (0.03%) aligned exactly 1 time
    861 (0.03%) aligned >1 times
0.06% overall alignment rate
```

Could you please help me with this?

Oops, I forgot to convert U to T in hairpin.fa file.. (so stupid about it..) Once I run it, I will confirm the result again.
Try to clip the adapter of the Illumina HiSeq 2000 miRNA protocol (TGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC)

And always check your read length distribution after clipping. There should be a peak at around 24nt.