This is a test version of Biostars. For the public version, visit https://www.biostars.org.
miRDeep2.pl cannot recognize reference fasta file

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
• 2,613 views • link
updated by Ram Ram • written by realnewbie • realnewbie

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

• 0 views • link
written by GenoMax GenoMax

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

• 0 views • link
written by realnewbie • realnewbie

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?

• 0 views • link
written by GenoMax GenoMax

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

• 0 views • link
written by realnewbie • realnewbie

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

• 0 views • link
written by realnewbie • realnewbie

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

• 0 views • link
written by GenoMax GenoMax

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,

• 0 views • link
written by realnewbie • realnewbie

0 answers

No answers yet.

Log in to answer this question.

More posts like this