Tag: mirdeep2

How to run quantifier from miRDeep2 (miRNA seqs from MirGeneDB) 0 Dear all, I want to perform miRNA quantification using quantifier.pl from miRDeep2. As default miRDeep2 is compatible with miRBase but I have to perform the quantification with mature and precursor sequences (fasta format) of miRNAs from MirGeneDB. I ran…

Jacobs L. Toxoplasma and toxoplasmosis. Annu Rev Microbiol. 1963;17:429–50. Article  CAS  PubMed  Google Scholar  Montoya JG, Liesenfeld O. Toxoplasmosis. The Lancet. 2004;363(9425):1965–76. Article  CAS  Google Scholar  Dubey JP. Duration of immunity to shedding of Toxoplasma gondii oocysts by cats. J Parasitol. 1995;81(3):410–5. Article  CAS  PubMed  Google Scholar  Dubey JP, Frenkel…

Need help regarding miRNA data analysis 0 Hi, I am currently working on miRNA data and have completed all the analyses using known miRNAs. Based on these, I have written a manuscript. However, I am facing difficulties when it comes to novel miRNAs, particularly with the naming issue, which prevents…

question related to novel mirna file from miRDeep2? 0 “Hi, Based on the attached JPG image of the miRDeep2 output file (novel miRNA), I have two questions: In the figure, there is a column labeled “Example miRBase miRNA with the same seed,” and under this column, there are several miRNAs…

Introduction Sarcoidosis is a multisystem inflammatory disease of unknown aetiology that is characterised by non-caseating epithelioid granulomatous lesions (aggregates of lymphocytes, macrophages, epithelioid cells, and giant cells).1 Typical clinical features include bilateral hilar lymph node lesions, pulmonary infiltration, and eye and skin lesions. Some patients may also have neurological and…

Participants This is an observational case–control study, carried out in adult patients who attended the Endocrinology and Nutrition Service of the Central University Hospital of Asturias, between June 2019 and December 2021. Written informed consent was obtained from all participants and the study was conducted in accordance with the principles…

mirdeep2- unable to extract files for mapping -extract_miRNAs: command not found error 0 Hi, i have installed mirdeep2 on ubuntu following the tutorial but unable to extract files from miRBase folder in the linux (the folder exists) . After giving the command extract_miRNAs hairpin.fa ssc > hairpin_ssc.fa, it showed extract_miRNAs:…

We are looking for pathogen miRNAs in host tissues among reads that couldn’t map to the host genome. The relevant commands are below; mapper.pl “$file”_HOST_UNMAPPED.fq -e -h -m -p $PathogenGenomeBasename -t “$file”_HOST_UNMAPPED_vs_PATHOGEN.arf -v -s “$file”_HOST_UNMAPPED_vs_PATHOGEN_COLLAPSED.fa miRDeep2.pl “$file”_HOST_UNMAPPED_vs_PATHOGEN_COLLAPSED.fa $PathogenGenomeBasename.fa HOST_UNMAPPED_vs_PATHOGEN.arf $PathogenMatureMiRNA $PathogenMiRNA $PathogenPrecursorMiRNA -c -d -g -1 According to this analysis…

mirdeep2 help 0 i have several RNA virus genomes and I am trying to find miRNA in the genomes, i am having trouble doing so i would love some help thanks mirdeep2 virus • 17 views • link updated 37 minutes ago by iraun 5.9k • written 1 hour ago…

Seeking Alternative Tools for Predicting Mature microRNAs from Vertebrate Animal Precursors in In Silico Study 0 Dear members of the forum, I am conducting an in silico study on vertebrate animals genomic data, in one of the steps I would have to predict mature microRNAs from their precursors. Despite attempting…

single- or pair-end small RNA seq for miRNAs? 1 Hi all! I’m in possession of a small RNA-seq dataset obtained from Illumina PE-50bp flow cell sequencing instead of SR-50bp flow cell. Does small RNA require sequencing to be single-end only (i.e. to detect miRNAs)? Can paired-end be used as well?…

Benelli G, Wilke A, Beier JC. Aedes albopictus (Asian Tiger Mosquito). Trends Parasitol. 2020;36:942–3. Article  Google Scholar  Bhatt S, Gething PW, Brady OJ, Messina JP, Farlow AW, Moyes CL, et al. The global distribution and burden of dengue. Nature. 2013;496:504–7. Article  CAS  Google Scholar  Bonizzoni M, Gasperi G, Chen X,…

miRDeep2 for small RNA sequencing 1 Hello, I am using the following tutorial for microRNA profiling: drmirdeep.github.io/mirdeep2_tutorial.html I was able to follow it until the patching step which is: bash patchme.sh However the next step where we install the miRBase reference file gives an error as follows: mirdeep2_patch abhaykanodia$ mirbase.pl…

Hello all, I have a directory with csv files (tab delimited). Each file have different sections (4 headers): miRDeep2 score novel miRNAs reported by miRDeep2 novel miRNAs, estimated false positives novel miRNAs, estimated true positives known miRNAs in species known miRNAs in data known miRNAs detected by miRDeep2 estimated signal-to-noise…

how to use mirdeep2 without a small RNA library 1 Hello everyone, I’m currenly working on a project where collecting tissue samples would be almost imposible… so we have to work with public data (reference genome and the RNA seq data that is already avaliable) and from what I’ve seen…

What does the part “mature miRBase miRNAs not detected by miRDeep2” actually mean in a miRDeep2 analysis? Should those hits be included in results? 0 After completion of a miRDeep2 analysis, the results are generated in three different parts, viz., 1) novel miRNAs predicted by miRDeep2, 2) mature miRBase miRNAs…

miRDeep2: Mapped reference id is not an id of the genome file genome_nowhitespace.fa 1 Hi everyone, I’m trying to run nf-co.re/smrnaseq pipeline and I’m having a problem with mirdeep2. Command: nextflow run nf-core/smrnaseq -profile ijcluster –input /home/794_both.fastq.gz –outdir /home/results –genome GRCh38 –protocol qiaseq –mature mirbase.org/ftp/CURRENT/mature.fa.gz –hairpin mirbase.org/ftp/CURRENT/hairpin.fa.gz Error message: Command…

Mirdeep2 Installation (Error In Make_Html.Pl) 1 Hi, I am trying to install mirdeep2. At the last step, I tested make_html.pl and error appeared as following: [liran@ip14-mp2 tools]$ make_html.pl Can’t locate PDF/API2.pm in @INC (@INC contains: /home/liran/tools/mirdeep2/lib64/perl5 /home/liran/tools/ViennaRNA-2.1.2/install_dir/lib64/perl5 /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at /home/liran/tools/mirdeep2/make_html.pl line 9. BEGIN failed–compilation…

miRDeep2.pl error in make_html2.pl 0 I have installed cpan install PDF::API2 And still got error Can’t locate PDF/API2.pm in @INC (@INC contains: /home/nbri/Tikshana/Ath/small_RNA/mirDeep/mirdeep2/lib/perl5 /home/nbri/vaishali/TOMATO_SRNA/new_analysis/mirdeep2-master/lib/perl5 /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64 /perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at /home/nbri/Tikshana/Ath/small_RNA/mirDeep/mirdeep2/bin/make_html2.pl line 25. BEGIN failed–compilation aborted at /home/nbri/Tikshana/Ath/small_RNA/mirDeep/mirdeep2/bin/make_html2.pl line 25 locate PDF/API2.pm /home/nbri/.cpan/build/PDF-API2-2.041-0/blib/lib/PDF/API2.pm /home/nbri/.cpan/build/PDF-API2-2.041-0/lib/PDF/API2.pm /home/nbri/.cpan/build/PDF-API2-2.041-1/blib/lib/PDF/API2.pm /home/nbri/.cpan/build/PDF-API2-2.041-1/lib/PDF/API2.pm /home/nbri/.cpan/build/PDF-API2-2.041-2/blib/lib/PDF/API2.pm…

what’s the criteria to select true-positive miRNAs predicted by miRDEEP2? 0 Hello all, What’s the criteria to select true-positive miRNAs predicted by miRDEEP2? As I understand, it requests significant randfold p-value labeled as yes, high miRDEEP2 score. Do you know a more clear criteria? Thanks. Xu miRDEEP2 true-positive criteria •…

How does miRdeep2 normalise sequences 1 Hi, I have mirdeep2 output that looks like this. #miRNA read_count precursor total seq seq(norm) mmu-let-7a-5p 43271 mmu-let-7a-1 43271 43271 7658.26 mmu-let-7a-1-3p 784 mmu-let-7a-1 784 784 138.76 mmu-let-7a-5p 43224 mmu-let-7a-2 43224 43224 7649.94 I think using the seq(norm) would be appropriate, but I cannot…