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7.1 years ago
jonessara770
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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
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.
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.
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?