Question: Tips for miRNA-Seq analysis
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gravatar for jonessara770
3.2 years ago by
jonessara770200
jonessara770200 wrote:

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 • 654 views
ADD COMMENTlink written 3.2 years ago by jonessara770200
1

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 REPLYlink written 3.2 years ago by h.mon30k

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 REPLYlink written 3.2 years ago by bioinforesearchquestions280

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 REPLYlink modified 10 days ago • written 10 days ago by Arindam Ghosh280
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