Question: miRNA alignment using bowtie 2
0
gravatar for anjuraas
22 months 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 • 1.2k views
ADD COMMENTlink modified 3 months ago by malu.gamarra0 • written 22 months ago by anjuraas10
1

Seems fine. What worries you?

ADD REPLYlink written 22 months ago by h.mon31k

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

ADD REPLYlink written 22 months 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 22 months ago by Buffo1.8k

It has given in the dataset its miRNA-seq.

ADD REPLYlink written 22 months ago by anjuraas10

Hello, I would like to know which commands you used because I do not know which parameters to choose, I am aligning with Bowtie (no Bowtie2) miRNA plants in front of the SARS-CoV-2 genome. Thanks a lot

ADD REPLYlink written 3 months ago by malu.gamarra0

Hello, I would like to know which commands you used because I do not know which parameters to choose, I am aligning with Bowtie (no Bowtie2) miRNA plants in front of the SARS-CoV-2 genome. Thanks a lot

ADD REPLYlink written 3 months ago by malu.gamarra0
1

Always start with default parameters. They are generally fine for most uses. Did you properly trim your samples first to remove adapters etc? miRNA are small (< 25 bp) so any extraneous sequences will cause problems with bowtie alignment.

ADD REPLYlink written 3 months ago by genomax89k
1
gravatar for h.mon
22 months ago by
h.mon31k
Brazil
h.mon31k 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 22 months ago by h.mon31k
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