Tips for miRNA-Seq analysis

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7.7 years ago

jonessara770 ▴ 240

Hi, I am new in miRNA-Seq analysis of human. would you please share your experience and any key elements that you think I should keep in mind while doing the analysis ( from sequence QC, alignment, quantification etc)?

Thanks

RNA-Seq • 1.5k views

ADD COMMENT • link 7.7 years ago by jonessara770 ▴ 240

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Key abilities are reading a lot (start reading here), and being curious. After that, you can start analyzing your data and ask more specific questions, which will very likely lead to excellent answers.

ADD REPLY • link 7.7 years ago by h.mon 35k

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Hi Jonessara,

Even I have started working on miRNA recently. I am pretty much new to this analysis.

1) Generally, miRNA will be 15 to 35 bases in length. I hope you might have generated at least 51 bases from the sequencing machine. So make sure you trim the 3'end of the sequenced reads where you might see Illumina adapter sequences being part of your sequenced reads.

2) You can download miRBase database and align it against them.

ADD REPLY • link 7.7 years ago by bioinforesearchquestions ▴ 370

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Like if I have a 50bp read do I need to compulsorily trim to 35bp or just remove the adapters?

And for alignment, for mRNA data I use hisat2 with Ensembl gtf file. The gtf file contains details of miRNA as well. So is it necessary to separately download annotations from other sources?

ADD REPLY • link 4.5 years ago by Arindam Ghosh ▴ 530

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