search

rajewsky-lab / mirdeep2

Discovering known and novel miRNAs from small RNA sequencing data
GNU General Public License v3.0
135 stars 49 forks source link

Consultation on the analysis pipeline for species that do not have mature and precursor miRNA sequences in the miRBase database #99

Closed wbc569668815 closed 2 years ago

wbc569668815 commented 2 years ago

Dear Developer Team: I have encountered some problems in the process of analyzing miRNA using mirDeep2 and hope to get your help. Questions are as follows:

  1. The species I am analyzing has reference genomes, but there are no mature miRNA sequences and precursor sequences in miRNAbase. I would like to know how to do the specific process. Do I only need to use the miRDeep2.pl script for new miRNA identification, and the required 3 fasta sequence inputs are "none, mature_ref_other_species.fa, none"?

    1. When using the mapper.pl script to align the sequencing data to the reference genome, why only 33% of the reads are aligned to the reference genome? The command was"mapper.pl reads.fa -c -j -l 18 -m -p cel_cluster -s reads_collapsed.fa -t reads_collapsed_vs_genome.arf -v" (because it is clean data, there is no connector, so I removed the "-k" parameter). And the reads.fa is 931Mb, while the reads_collapsed.fa is only 53.9Mb. When I used the same sequencing data to align with the reference genome using bowtie software, the alignment rate was over 80%.

Looking forward to hearing from you, I would be very grateful.

wbc569668815 commented 2 years ago

Thanks again. I would be grateful for your reply.

Drmirdeep commented 2 years ago

This is a pure bug tracker. If you need help with your analyses have a look somewhere else. A good starting point are the mirdeep(2) publications and the tutorial folder.

wbc569668815 commented 2 years ago

Dear Sebastian Mackowiak,

I have read the readme and followed the Script Reference before analyzing. I read all the Example uses, but there is no example similar to my case.

I provided the command parameters I used on Github, could you tell me why the error occurs? My sequencing data is 931Mb, while reads_collapsed.fa is only 53.9Mb, and the mapping rate is only 33%. Is this normal?

Thanks for your reply.

Best wishes.

Bingchao

edit (@mschilli87): Removed email footer and quote.

Drmirdeep commented 2 years ago

Again, we don't do consulting. If this is normal or not depends on your data. QC of the input data is done by the user not us. If the mapping rate is low then you need to check your data. The tool apparently works since otherwise there would be no output. You can check all intermediate files created by the mapper tool. If you find a read that maps with your bowtie mapping but not with the mapper.pl you will likely find the reason why it is not mapping.