miRDeep2.pl cannot recognize reference fasta file
0
0
Entering edit mode
4.4 years ago
realnewbie ▴ 30

Hi,

I have been trying to run mirdeep2 for a while. However, the tool cannot recognize bowtie-indexed reference genome at mirdeep2.pl step. It gives the same error: "refence.fa is not a fasta file". However it runs same file for mapping. When it comes to mirdeep2.pl, it could not. I could not understand why. Even little help will be appreacited a lot. Thanks a lot!

mirdeep2 fasta mirna mirdeep2.pl mirna-sequencing • 1.6k views
ADD COMMENT
0
Entering edit mode

Are you using plain fasta file? You can't use bowtie indexed genome.

ADD REPLY
0
Entering edit mode

What is "plain fasta" file? I have been using this: Homo_sapiens.GRCh37.dna.primary_assembly.fa. In tutorial, it says we need to index the fasta file first.

For novel miRNA prediction we need to map the reads against a reference database which has to be indexed by bowtie 1. For this we take a reference database file, lets call it refdb.fa (This can be a genome file or simply a file with scaffolds) and build a bowtie index by typing

From this site: https://drmirdeep.github.io/mirdeep2_tutorial.html

ADD REPLY
0
Entering edit mode

If you followed instructions in the tutorial I suppose you used

bowtie-build Homo_sapiens.GRCh37.dna.primary_assembly.fa Homo_sapiens.GRCh37.dna.primary_assembly.fa

Here Homo_sapiens.GRCh37.dna.primary_assembly.fa should be the original fasta format genome file. Are all result files from bowtie-build command in the same directory?

ADD REPLY
0
Entering edit mode

Yes, they are in the same directory. By the way, thanks a lot for your quick response to help.

ADD REPLY
0
Entering edit mode

Tutorial page sucks. It was not useful at all. It was impossible to download the relevant files properly without conda install.

ADD REPLY
1
Entering edit mode

You may want to follow this tutorial. The files referred to there are probably in the tutorial directory in miRdeep2 installation.

ADD REPLY
0
Entering edit mode

Thanks a lot! I realized that in the mapper we are using bowtie indexed reference genome, however, in the mirdeep.pl step, we need to use not indexed-original fasta file. The old tutorial was a little bit confusing regarding this issue. New tutorial is more helpful. Best,

ADD REPLY

Login before adding your answer.

Traffic: 2939 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6