Tweet
Mapping to miRBase
Hi guys,
How to do the mapping to miRBase to identify human miRNAs?
1. At first you should download 2 fasta files from the website: http://www.mirbase.org/ftp.shtml (and merge them into one file):
hairpin.fa Fasta format sequences of all miRNA hairpins
mature.fa Fasta format sequences of all mature miRNA sequences
3. Then, you should generate gtf for Bowtie 1 (if you want to use specifically Bowtie 1) or gff for Htseq (based on the downloaded fasta files).
I did the analysis this way, but I received very strange results (for example mir-8689, mir-7689 - I mean miRNAs with very high numbers) instead of what I was expecting (mir9, mir31, etc.- miRNAs with much smaller numbers).
Do you know maybe what I could do wrongly?
Thanks for your answer in advance!
How to do the mapping to miRBase to identify human miRNAs?
1. At first you should download 2 fasta files from the website: http://www.mirbase.org/ftp.shtml (and merge them into one file):
hairpin.fa Fasta format sequences of all miRNA hairpins
mature.fa Fasta format sequences of all mature miRNA sequences
3. Then, you should generate gtf for Bowtie 1 (if you want to use specifically Bowtie 1) or gff for Htseq (based on the downloaded fasta files).
I did the analysis this way, but I received very strange results (for example mir-8689, mir-7689 - I mean miRNAs with very high numbers) instead of what I was expecting (mir9, mir31, etc.- miRNAs with much smaller numbers).
Do you know maybe what I could do wrongly?
Thanks for your answer in advance!
Comment