How can I Annotate my miRNA data against MirBase?

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7.3 years ago

k.kathirvel93 ▴ 310

Hi All, Can anyone help? How can I annotate my microRNA data against MirBase. Initially, my microRNA data were mapped against the reference genome by Bowtie2, and sam file were converted into bam and sorted by picard. Now i want to get to know, how do i annotate my bam file against mirbase database. Thanks in advance.

K.Kathir

RNA-Seq Assembly genome sequence next-gen • 2.0k views

ADD COMMENT • link updated 7.2 years ago by Biostar 20 • written 7.3 years ago by k.kathirvel93 ▴ 310

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what is "how do i annotated my bam file against mirbase database" ? what kind of output do you need ?

ADD REPLY • link 7.3 years ago by Pierre Lindenbaum 164k

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From bam file(s), assuming that there are controls and cases, get a list of deferentially expressed and statistically significant miRNAs. Then you can use miRbase. To get significant miRNA between groups (controls and cases), follow some thing like here: http://miarmaseq.cbbio.es/

ADD REPLY • link 7.3 years ago by cpad0112 21k

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