Tag: mirdeep2

miRDeep2 for small RNA sequencing

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…

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Merging csv files with specific headers

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…

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how to use mirdeep2 without a small RNA library

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…

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What does the part “mature miRBase miRNAs not detected by miRDeep2” actually mean in a miRDeep2 analysis? Should those hits be included in results?

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…

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Mapped reference id is not an id of the genome file genome_nowhitespace.fa

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…

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Mirdeep2 Installation (Error In Make_Html.Pl)

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…

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miRDeep2.pl error in make_html2.pl

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…

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what’s the criteria to select true-positive miRNAs predicted by miRDEEP2?

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 •…

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How does miRdeep2 normalise sequences

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…

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