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?
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.
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Seems fine. What worries you?
thank you for your reply. someone told me alignment rate of miRNA should be below 50%.so I got confused..
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.
It has given in the dataset its miRNA-seq.
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
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
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.