Hi,
I have run a miseq run for microrna detection, filtered the data (removed adaptors and ncRNAs (others than microRNAs) and i´m now going to identify reads mapping to microRNAs in Human.
As for the strategy not sure if i have to map to the human genome or i can directly map to the mature.fa database from mirbase. Any suggestion ? The reason i have choosen not to map to the human genome is that not really interested in denovo microRNAS but on the contrary i´m not sure if i have first to remove reads that can map to other parts of the genome.
So far i have decided to align to mature mirbase database.
I´m using the following command:
bbduk.sh ref=mature.fa.gz in=1.fa.gz stats=statsmature.txt out=mirna.fa hdist=0
1/ What is the best approach to identify full match microRNAs (no mismatch) with bbduk.
2/ How to identify isomirs ? Do i need to cluster reads first with vsearch with a 99% identity and then map to mirbase with 100% full match.
Thanks for your comments
I have run a miseq run for microrna detection, filtered the data (removed adaptors and ncRNAs (others than microRNAs) and i´m now going to identify reads mapping to microRNAs in Human.
As for the strategy not sure if i have to map to the human genome or i can directly map to the mature.fa database from mirbase. Any suggestion ? The reason i have choosen not to map to the human genome is that not really interested in denovo microRNAS but on the contrary i´m not sure if i have first to remove reads that can map to other parts of the genome.
So far i have decided to align to mature mirbase database.
I´m using the following command:
bbduk.sh ref=mature.fa.gz in=1.fa.gz stats=statsmature.txt out=mirna.fa hdist=0
1/ What is the best approach to identify full match microRNAs (no mismatch) with bbduk.
2/ How to identify isomirs ? Do i need to cluster reads first with vsearch with a 99% identity and then map to mirbase with 100% full match.
Thanks for your comments
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