Hello
Can i do a DEG with Mir-seq data with this method ?
1/ mapping my data with human reference genome
2/ annotated miRNA locations with the result, (this way i get rid of the rRNA, tRNA and other small rna which i dont need in my analysis)
is this correct ?
This means you are wondering if you can simply determine the overlaps between the alignments and the annotated miRNA and go from there? If you are only interested in miRNA thats the way to go. I guess you would also want to consider their targets. Additionally you should further screen the loci for repetitive elements.
Richard A. Schäfer I saw in some workflows, they use Collapse in their work, But some one in Biostar inform me to not use that tool. should i do it in this workflow ? And if you can explain why even they use Collapse
Thank you
You should simply use the human miRNAome as your reference. Map against this reference and count reads using eg star aligner. In this case you dont have to temove any other kinds of small RNAs. Only the miRNAs will be mapped and counted. Then use DESeq to carry out the differental expression analysis between the groups of samples you want to compare.
Rune Andreassen Thanks for your reply. Do you have a valid link about this Human Mirnaome reference. i just download mirna annotation from ucsc. but i didnt heard about mirnaome as a reference.
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