Question: miRNA alignment using bowtie 2
0
gravatar for anjuraas
9 weeks ago by
anjuraas10
anjuraas10 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 • 210 views
ADD COMMENTlink modified 9 weeks ago by h.mon22k • written 9 weeks ago by anjuraas10
1

Seems fine. What worries you?

ADD REPLYlink written 9 weeks ago by h.mon22k

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

ADD REPLYlink written 9 weeks ago by anjuraas10

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 9 weeks ago by Buffo1.2k

It has given in the dataset its miRNA-seq.

ADD REPLYlink written 7 weeks ago by anjuraas10
0
gravatar for h.mon
9 weeks ago by
h.mon22k
Brazil
h.mon22k 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 9 weeks ago by h.mon22k
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