Tag: mirdeep2

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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