Question: miRNA alignment using bowtie 2
0
gravatar for anjuraas
11 days ago by
anjuraas0
anjuraas0 wrote:

i aligned miRNA against human genome 38 using bowtie2 after trimming and got an alignment rate of >90%.Is this normal? What should be the alignment rate of miRNA?

alignment genome • 101 views
ADD COMMENTlink modified 8 days ago by h.mon21k • written 11 days ago by anjuraas0
1

Seems fine. What worries you?

ADD REPLYlink written 11 days ago by h.mon21k

thank you for your reply. someone told me alignment rate of miRNA should be below 50%.so I got confused..

ADD REPLYlink written 11 days ago by anjuraas0

Since your high alignment rate may be no surprinsing, you would check if your reads really correspond to miRNAs, short RNA is not a miRNA by default, but also I recommend you to perform ungapped alingnments with bowtie2 or use Bowtie(1) to avoid isomirs.

ADD REPLYlink written 8 days ago by Buffo1.2k
0
gravatar for h.mon
8 days ago by
h.mon21k
Brazil
h.mon21k wrote:

Hi anjuraas , you should elaborate more your questions, providing more details (e.g. the commands you used, summary output of bowtie2) and the reason why you think 90% mapping rate is not expected.

miRNA mapping rate may vary for a lot of reasons. The paper Evaluation of microRNA alignment techniques has some hints on some of the reasons. In general, I would expect: high mapping rate, but also high multi-mapping rate.

someone told me alignment rate of miRNA should be below 50%. so I got confused.

And why it should be bellow 50%? "Someone told me so" isn't a good answer. Indeed, your mapping rate seems too high, I think more common is something in the range 50-75%. You can map your miRNA against miRbase, this will provide a quality control and annotation of your miRNAs.

ADD COMMENTlink written 8 days ago by h.mon21k
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