UMI RNASeq data analysis

Question

[struggler]

I am analysing UMI small RNASeq data for miRNA prediction. I used miRDP2 for novel miRNA prediction with default parameters. Can any one suggest me how to proceed for novel miRNA expression analysis?

Answer 1

[kanika.151]

I hope this helps.

miRNA analysis pipeline

[struggler]

Thanks Kanika, I have looked into it but this pipeline use mirDeep2. And I am using miRDP2 (for plant), for expression analysis I am not sure how to get count values from mirDP2 output. Although I have tried following approach: 1>made database for predicted novel miRNA 2> map all filtered read over it 3> sam file to count file by samtools. 4> plot PCA But PCA plot does not any biological relevant pattern/distribution among the sample. Could anyone suggest how get count value from miRDP2 output or another way for novel expression analysis?