Tag: MiRBase

Page not found at /mature/MIMAT0027893?acc=MIMAT0027893

Page not found at /mature/MIMAT0027893?acc=MIMAT0027893 Using the URLconf defined in mirbase_new.urls, Django tried these URL patterns, in this order: __debug__/ admin/ [name=”home”] __debug__/ ajax/draw_reads_plot/<slug:accession> [name=”ajax_draw_reads_plot”] ajax/draw_reads_plot_mismatch/<slug:accession> [name=”ajax_draw_reads_plot_mismatch”] ajax/load-chromosomes/ [name=”ajax_load_chromosomes”] ajax/load-tissues/ [name=”ajax_load_tissues”] ajax/load-experiments/ [name=”ajax_load_experiments”] ajax/load-hairpins-for-mature/ [name=”ajax_load_hairpins_for_mature”] ajax/load-papers/ [name=”ajax_load_papers”] ajax/page-clusters/ [name=”ajax_page_clusters”] ajax/load-clusters/ [name=”ajax_load_clusters”] ajax/load-sentences/ [name=”ajax_load_sentences”] ajax/load-reads/ [name=”ajax_load_reads”] ajax/load-reads-mismatches/ [name=”ajax_load_reads_mismatches”] ajax/load-results/ [name=”ajax_load_results”] ajax/get-sequences/…

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QIAseq miRNA 96 Index Kit IL UDI-B (96)

Gel-free miRNA Sample to Insight solution for differential expression analysis and novel discovery using next-generation sequencing Features Gel-free miRNA sequencing library prep from as little as 1 ng of total RNA Elimination of adapter dimers and unwanted RNA species resulting in the highest fidelity and most efficient data Integrated Unique…

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Opinion on miRNA pipeline

Opinion on miRNA pipeline 0 Dear colleagues, I am currently in the process of evaluating miRNA Seq data and would like to present my pipeline for your review. Given the absence of a dedicated bioinformatician in my department, particularly for this specific use case, I am eager to gather feedback…

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Salpa genome and developmental transcriptome analyses reveal molecular flexibility enabling reproductive success in a rapidly changing environment

Loeb, V. et al. Effects of sea-ice extent and krill or salp dominance on the Antarctic food web. Nature 387, 897–900 (1997). Article  ADS  CAS  Google Scholar  Atkinson, A., Siegel, V., Pakhomov, E. & Rothery, P. Long-term decline in krill stock and increase in salps within the Southern Ocean. Nature…

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Extracting list of identical items from several excel files

Extracting list of identical items from several excel files 0 Hi guys, I have 10 excel files with several columns and rows. The column headers are similar in all file but for the rows some items are similar while others are not. Below is an excerpt for one of the…

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Analysis of nucleoporin 107 overexpression

Introduction Lung cancer is one of the most common types of cancer worldwide and the leading cause of cancer death.1 The main category of lung cancer is non-small cell lung cancer, accounting for about 85%, and lung adenocarcinoma, as a kind of non-small cell lung cancer, is the most frequently…

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When will RNA get its AlphaFold moment? | Nucleic Acids Research

Abstract The protein structure prediction problem has been solved for many types of proteins by AlphaFold. Recently, there has been considerable excitement to build off the success of AlphaFold and predict the 3D structures of RNAs. RNA prediction methods use a variety of techniques, from physics-based to machine learning approaches….

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How to deal with mirdeep2 output “miRBase miRNAs not detected by miRDeep2”

How to deal with mirdeep2 output “miRBase miRNAs not detected by miRDeep2” 0 Hi guys, I have successfully ran mirdeep2 and I have gotten three sets of results including: novel, known mature and miRBase miRNAs not detected by miRDeep2. I understand that the third group (miRBase miRNAs not detected by…

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Page not found at /mature/MIMAT0027472?acc=MIMAT0027472

Page not found at /mature/MIMAT0027472?acc=MIMAT0027472 Using the URLconf defined in mirbase_new.urls, Django tried these URL patterns, in this order: __debug__/ admin/ [name=”home”] __debug__/ ajax/draw_reads_plot/<slug:accession> [name=”ajax_draw_reads_plot”] ajax/draw_reads_plot_mismatch/<slug:accession> [name=”ajax_draw_reads_plot_mismatch”] ajax/load-chromosomes/ [name=”ajax_load_chromosomes”] ajax/load-tissues/ [name=”ajax_load_tissues”] ajax/load-experiments/ [name=”ajax_load_experiments”] ajax/load-hairpins-for-mature/ [name=”ajax_load_hairpins_for_mature”] ajax/load-papers/ [name=”ajax_load_papers”] ajax/page-clusters/ [name=”ajax_page_clusters”] ajax/load-clusters/ [name=”ajax_load_clusters”] ajax/load-sentences/ [name=”ajax_load_sentences”] ajax/load-reads/ [name=”ajax_load_reads”] ajax/load-reads-mismatches/ [name=”ajax_load_reads_mismatches”] ajax/load-results/ [name=”ajax_load_results”] ajax/get-sequences/…

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Alignment of mirna on specific organism data from mirbase

Alignment of mirna on specific organism data from mirbase 0 I have micro-RNA sequences that I need to align specifically to Drosophilar melanogaster mature microRNA from mirbase using bowtie. Have realized the fasta sequence of mature miRNA in mirbase contain all the organisms that whose microRNAs have been sequenced and…

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miRBase entry: hsa-mir-30a

PubMed ID: 11679670 Identification of novel genes coding for small expressed RNAs “Lagos-Quintana M, Rauhut R, Lendeckel W, Tuschl T”“Science (2001) 294:853-858 PubMed ID: 14573789 Reduced accumulation of specific microRNAs in colorectal neoplasia “Michael MZ, O’ Connor SM, van Holst Pellekaan NG, Young GP, James RJ”“Mol Cancer Res (2003) 1:882-891…

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miRBase entry: hsa-mir-21

PubMed ID: 11679670 Identification of novel genes coding for small expressed RNAs “Lagos-Quintana M, Rauhut R, Lendeckel W, Tuschl T”“Science (2001) 294:853-858 PubMed ID: 15183728 Human embryonic stem cells express a unique set of microRNAs “Suh MR, Lee Y, Kim JY, Kim SK, Moon SH, Lee JY, Cha KY, Chung…

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How to run quantifier from miRDeep2 (miRNA seqs from MirGeneDB)

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…

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CluePedia Cytoscape plugin: pathway insights using integrated experimental and in silico data | Bioinformatics | Oxford Academic | A travel guide to Cytoscape plugins

Synopsis Summary: The CluePedia Cytoscape plugin is a search toolbar for new markers potentially associated to pathways. CluePedia calculates linear furthermore non-linear statistical dependencies from experimenta data. Genes, proteinaceous and miRNAs can be connected founded on within silico and/or experimentally information and integrated into a ClueGO network of terms/pathways. Interrelations…

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miRBase – Downloads

miRBase – Downloads Downloads README – Release notes – read these first! miRNA.dat – All published miRNA data in EMBL format hairpin.fa – Fasta format sequences of all miRNA hairpins mature.fa – Fasta format sequences of all mature miRNA sequences miRNA.diff – Changes between the last release and this miRNA.dead…

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multiple alignments and seed length vs read length in miRNA mapping

Bowtie – multiple alignments and seed length vs read length in miRNA mapping 0 Hi everyone, I have miRNA reads with a mean length of 21bp. I want to map these reads onto human miRNA reference sequences (miRBase) that have a mean length of 22bp (ranging from 16bp – 28bp)….

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miRCarta – miRBase precursor

Accession MI0015896 Name hsa-mir-4288 similar to following miRCarta precursors hsa-2258.1 Organism Homo sapiens Genome GRCh38.p10 Location chr8:28,505,116-28,505,182 (-) miRNA hsa-miR-4288 Sequence (5′ -> 3′)(67 nts) AUGGAGGUGGAGAGUCAUCAGCAGCACUGAGCAGGCAGUGUUGUCUGCUGAGUUUCCACGUCAUUUG MFE -34.50 kcal/mol first miRBase version 15.0 last miRBase version 21.0 Clusters (10 kb)(1 precursors) hsa-mir-4288 Experiments External DBs Read more here: Source link

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html – SJTUG Mirror Index

.. BSgenome.Amellifera.BeeBase.assembly4.html BSgenome.Amellifera.UCSC.apiMel2.html BSgenome.Athaliana.TAIR.01222004.html BSgenome.Athaliana.TAIR.04232008.html BSgenome.Btaurus.UCSC.bosTau3.html BSgenome.Btaurus.UCSC.bosTau4.html BSgenome.Celegans.UCSC.ce2.html BSgenome.Cfamiliaris.UCSC.canFam2.html BSgenome.Dmelanogaster.UCSC.dm2.html BSgenome.Dmelanogaster.UCSC.dm3.html BSgenome.Drerio.UCSC.danRer5.html BSgenome.Ecoli.NCBI.20080805.html BSgenome.Ggallus.UCSC.galGal3.html BSgenome.Hsapiens.UCSC.hg17.html BSgenome.Hsapiens.UCSC.hg18.html BSgenome.Hsapiens.UCSC.hg19.html BSgenome.Mmusculus.UCSC.mm8.html BSgenome.Mmusculus.UCSC.mm9.html BSgenome.Ptroglodytes.UCSC.panTro2.html BSgenome.Rnorvegicus.UCSC.rn4.html BSgenome.Scerevisiae.UCSC.sacCer1.html BSgenome.Scerevisiae.UCSC.sacCer2.html GGHumanMethCancerPanelv1.db.html GO.db.html Hs6UG171.db.html HuExExonProbesetLocationHg18.html HuExExonProbesetLocationHg19.html HuO22.db.html IlluminaHumanMethylation27k.db.html JazaeriMetaData.db.html KEGG.db.html LAPOINTE.db.html Masks.Dmelanogaster.UCSC.dm3.html MoExExonProbesetLocation.html Mu15v1.db.html Mu22v3.db.html Norway981.db.html OperonHumanV3.db.html PFAM.db.html POCRCannotation.db.html PartheenMetaData.db.html RaExExonProbesetLocation.html RmiR.Hs.miRNA.html RmiR.hsa.html Roberts2005Annotation.db.html SHDZ.db.html SNPlocs.Hsapiens.dbSNP.20071016.html SNPlocs.Hsapiens.dbSNP.20080617.html SNPlocs.Hsapiens.dbSNP.20090506.html…

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Design of crRNA to Regulate MicroRNAs Related to Metastasis in Colorectal Cancer Using CRISPR-C2c2 (Cas13a) Technique

Colorectal cancer (CRC) is the third most prevalent cancer with the second-highest mortality rate worldwide. microRNAs (miRNAs) of cancer-derived exosomes have shown promising diagnosis potential. Recent studies have shown the metastatic potential of a specific group of microRNAs called metastasis. Therefore, down-regulation of miRNAs at the transcriptional level can reduce…

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question related to novel mirna file from miRDeep2?

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…

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Biomedicines | Free Full-Text | High-Accuracy ncRNA Function Prediction via Deep Learning Using Global and Local Sequence Information

1. Introduction In recent years, growing access to massive transcriptome sequencing technologies has led to the discovery of an increasing number of novel transcripts from various species. The majority of these transcripts result in non-coding ribonucleic acid (ncRNA) molecules, short sequences of RNA that, with the exception of a small…

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featurecounts not working on mirbase annotation file

featurecounts not working on mirbase annotation file 0 Hello I am trying to analyze miRNA-seq data but I am having problems with the mapping. I always get pretty much 0 counts with the built in annotation file, so I got one from miRBase. However, I always get an error when…

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Human bone marrow-derived mesenchymal stem overexpressing microRNA-124-3p inhibit DLBCL progression by downregulating the NFATc1/cMYC pathway | Stem Cell Research & Therapy

Microarray-based expression analysis and GEO database analysis The DLBCL-related miRNA expression profiles of GSE29493 and GSE40239 were retrieved from the Gene Expression Omnibus (GEO) database (www.ncbi.nlm.nih.gov/geo/). MiR-124’s pan cancer analysis is conducted through online websites (www.picb.ac.cn/dbDEMC/). Bioinformatics predicted NFATc1 as the target of miR-124-3p The miRbase (www.mirbase.org/), miRDB (mirdb.org), and…

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Circulating miRNA expression in long-standing type 1 diabetes mellitus

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…

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Bioinformatics-Based Identification of CircRNA-MicroRNA-mRNA Network for Calcific Aortic Valve Disease

Background. Calcific aortic valve disease (CAVD) is the most common native valve disease. Valvular interstitial cell (VIC) osteogenic differentiation and valvular endothelial cell (VEC) dysfunction are key steps in CAVD progression. Circular RNA (circRNAs) is involved in regulating osteogenic differentiation with mesenchymal cells and is associated with multiple disease progression,…

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mirdeep2- unable to extract files for mapping -extract_miRNAs: command not found error

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:…

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Characterizing expression changes in noncoding RNAs during aging and heterochronic parabiosis across mouse tissues

Mapping of ncRNA expression across mouse organs We sequenced 771 tissue samples of the TMS cohort to map molecular shifts across the whole organism during healthy aging (Fig. 1a). The protocol enriches for small ncRNA, especially mature miRNAs. Even though full-length reads cover only small ncRNAs (miRNAs or piwi-interacting RNAs…

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Bioconductor – Ularcirc

DOI: 10.18129/B9.bioc.Ularcirc     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see Ularcirc. Shiny app for canonical and back splicing analysis (i.e. circular and mRNA analysis) Bioconductor version: 3.13 Ularcirc reads in STAR aligned splice junction files and provides visualisation and analysis tools…

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Comprehensive analysis of circular RNAs in porcine small intestine epithelial cells associated with susceptibility to Escherichia coli F4ac diarrhea | BMC Genomics

Ren J, Yan X, Ai H, Zhang Z, Huang X, Ouyang J, Yang M, Yang H, Han P, Zeng W, et al. Susceptibility towards enterotoxigenic Escherichia coli F4ac diarrhea is governed by the MUC13 gene in pigs. PLoS ONE. 2012;7(9):e44573. Article  CAS  PubMed  PubMed Central  Google Scholar  Guinée P, Jansen…

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Count miRNA reads from gtf file

Hi There! I performed count reads by usinf FeatureCounts by using annotation file gff miRBase and Lawson’s gtf annotation file (here). I have 3 replicates for each sample ( n = 3). The count reads based on miRBase annotation shows one outlier replicate in one of my sample on DESEQ2…

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fRNC: Uncovering the dynamic and condition-specific RBP-ncRNA circuits from multi-omics data

Comput Struct Biotechnol J. 2023; 21: 2276–2285. ,a,1 ,a,1 ,a ,b,c and a,b,⁎ Leiming Jiang aComputational Systems Biology Laboratory, Department of Bioinformatics, Shantou University Medical College (SUMC), 515041 Shantou, China Shijia Hao aComputational Systems Biology Laboratory, Department of Bioinformatics, Shantou University Medical College (SUMC), 515041 Shantou, China Lirui Lin aComputational…

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miRCarta – miRBase miRNA

Accession m-223 Sequence (5′ -> 3′) (21 nts)  UGACCGAUUUCUCCUGGUGUU Sequence (5′ -> 3′) with flanks CUGACCGAUUUCUCCUGGUGUUCAG similar to miRNAs from miRBase bta-miR-29d-5p (MIMAT0026919)chi-miR-29c-5p (MIMAT0036116)hsa-miR-29c-5p (MIMAT0004673)mmu-miR-29c-5p (MIMAT0004632)rno-miR-29c-5p (MIMAT0003154) Located in precursor bta-223-27771.1Chr16:77,562,553-77,562,573 (+) MFE -2.60 kcal/mol first miRCarta version 1.0 last miRCarta version 1.1 Read more here: Source link

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Bioinformatics Analysis of Small RNA Sequencing

Small RNAs are important functional molecules in organisms, which have three main categories: microRNA (miRNA), small interfering RNA (siRNA), and piwi-interacting RNA (piRNA). They are less than 200 nt in length and are often not translated into proteins. Small RNA generally accomplishes RNA interference (RNAi) by forming the core of…

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RIP Sequencing Q&A – CD Genomics

General Questions What information should I know before I do the RIP-Seq? Before doing a RIP-SEQ you generally need to specify • The type of sample to be done • What RBPs are of interest • Whether IP-level antibodies are available for these RBPs • The type…

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ncRNA | Free Full-Text | Insights into Online microRNA Bioinformatics Tools

2. MicroRNA Biogenesis and Targeting MiRNAs are small non-coding single-stranded RNAs encoded within non-coding sequences of the genome; however, a minority of miRNAs are known to also be encoded within exons [3]. Interestingly, miRNAs located within intronic regions of protein-coding genes can be transcribed from the same promoter as a…

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small RNA Workflow

small RNA Workflow 1 Hello World ! Looking forward a solution reagarding choosing best small RNA workflows(pre-processing->results/reports) based on following perspectives Execution Mode : Linux based, Standalone with command line mode. Not web-based. Organism : Insects Based on reviews : mimiARma-Seq | The UEA sRNA Workbench | SePIA | CAP-miRSeq…

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Blastocystis and Chronic Spontaneous Urticaria: Possible microRNA-based Mechanisms

The following is a summary of “Possible microRNA-based mechanism underlying relationship between chronic spontaneous urticaria and Blastocystis,” published in the December 2022 issue of Experimental Parasitology by Örsten, et al. Extraintestinal clinical symptoms, such as urticaria etiology, have been linked to Blastocystis spp. This study aimed to compare the microRNA…

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mirbase does not have miRNA annotation of my species, what are the alternatives?

mirbase does not have miRNA annotation of my species, what are the alternatives? 1 Hello I have been trying to align E. coli mirnome data. For other species, I see that many people have suggested to use the data available on mirbase to use as reference, but it doesn’t have…

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Whole-transcriptome profiling across different developmental stages of Aedes albopictus (Diptera: Culicidae) provides insights into chitin-related non-coding RNA and competing endogenous RNA networks | Parasites & Vectors

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,…

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microRNAs not available in TxDb.Hsapiens.UCSC.hg38.knownGene

microRNAs not available in TxDb.Hsapiens.UCSC.hg38.knownGene 0 @lluis-revilla-sancho Last seen 8 hours ago European Union I was looking to some examples and I could retrieve the microRNAs of the hg19 transcriptome, but not from the hg38 transcript annotation. I realized this might be because TxDb.Hsapiens.UCSC.hg38.knownGene doesn’t have a miRBase build ID,…

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Assessing spermatozoal small ribonucleic acids and their relationship to blastocyst development in idiopathic infertile males

Vander, B. M. & Wyns, C. Fertility and infertility: Definition and epidemiology. Clin. Biochem. 62, (2018). Sun, H. et al. Global, regional, and national prevalence and disability-adjusted life-years for infertility in 195 countries and territories, 1990–2017: Results from a global burden of disease study, 2017. Aging 11, 10952 (2019). Article …

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Nomascus leucogenys (northern white-cheeked gibbon) nle-miR-34a

Javascript is currently disabled or is not supported by this browser. Please enable JavaScript for full functionality. Sorry, there was a problem loading sequence from server. Please try again and contact us if the problem persists. Nomascus leucogenys (northern white-cheeked gibbon) nle-miR-34a URS000030BD69_61853 Automated summary: This miRNA sequence is 22…

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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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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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assign in pandas pipeline – DevDreamz

You can use pipe: tmp_df = df.\ drop(“Gene type”, axis=1).\ rename(columns = { “Gene stable ID”: “ENSG”, “Gene name”: “gene_name”, “miRBase accession”: “MI”, “miRBase ID”: “mirna_name” }).\ pipe(lambda x: x.assign(species = x.mirna_name.str[:3])) tmp_df Out[365]: ENSG gene_name MI mirna_name species 0 ENSG00000274494 MIR6832 MI0022677 hsa-mir-6832 hsa 1 ENSG00000283386 MIR4659B MI0017291 hsa-mir-4659b…

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Htseq is giving me 0 counts using the GFF3 of miRBase

Hello! I am trying to annotate a miRNA-seq so that it gives me mature miRNAs where I already have 5p and 3p. For this, I have used the index mm10.fa and the miRBase mmu.gff3. I have aligned with HISAT2 and am trying to count with HTSeq, however I get 0…

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Extracellular circulating miRNAs as stress-related signature to search and rescue dogs

Study approval was provided by the Research Ethics Committee of the University of Perugia (report n.2018-21 of 11/12/2018) according to Italian Ministry of Health legislation18. All methods were carried out following relevant guidelines and regulations and the study was carried out in compliance with the ARRIVE guidelines. Informed consent is…

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UMItools dedup deduplication taking too much time + RAM

I have some RNAseq data from miRNAs that I have processed with Bowtie2 (aligning to miRBase). Now, when doing the deduplication with umi_tools dedup I find that some of the files take a lot of time+RAM to finish (some files take around 3-4 minutes and 4-5GB of RAM and some…

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mirbase ftp error

mirbase ftp error 0 When I am running this link “wget mirbase.org/pub/mirbase/21/hairpin.fa.gz” in the terminal the below error is appearing for me. How can I fix it? -2022-01-21 16:35:30– mirbase.org/pub/mirbase/21/hairpin.fa.gz => ‘hairpin.fa.gz’ Resolving mirbase.org (mirbase.org)… 130.88.97.249 Connecting to mirbase.org (mirbase.org)|130.88.97.249|:21… failed: Connection refused. ftp mirbase • 225 views • link…

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Bioconductor – mirbase.db

DOI: 10.18129/B9.bioc.mirbase.db     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see mirbase.db. miRBase: the microRNA database Bioconductor version: 3.11 miRBase: the microRNA database assembled using data from miRBase (www.mirbase.org/). Author: James F. Reid <reidjf at gmail.com> Maintainer: James F. Reid <reidjf at…

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assign in pandas pipeline – Stackify

You can use pipe: tmp_df = df. drop(“Gene type”, axis=1). rename(columns = { “Gene stable ID”: “ENSG”, “Gene name”: “gene_name”, “miRBase accession”: “MI”, “miRBase ID”: “mirna_name” }). pipe(lambda x: x.assign(species = x.mirna_name.str[:3])) tmp_df Out[365]: ENSG gene_name MI mirna_name species 0 ENSG00000274494 MIR6832 MI0022677 hsa-mir-6832 hsa 1 ENSG00000283386 MIR4659B MI0017291 hsa-mir-4659b…

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Omics advanced 07 | transcriptome mRNA | miRNA | lncrna

A brief introduction mRNA,miRNA,lncRNA And circRNA Principle of genome sequencing 、 Routine analysis of Shengxin . Catalog Introduction to transcriptome sequencing mRNA|miRNA|lncRNA|circRNA Introduction to analysis mRNA Group miRNA Group lncRNA Group circRNA Group mRNA|miRNA|lncRNA|circRNA Correlation analysis Reference Introduction to transcriptome sequencing Transcriptome (Transcriptome) Is a single or group of cells…

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Biostar Systems

Comment: STAR vs Novoalign IGV Browser visualization by chasem &utrif; 10 That is good to know that it isn’t just my set of reads…still concerning, though. Comment: STAR vs Novoalign IGV Browser visualization by chasem &utrif; 10 I was not expecting this — not sure what to make of it…

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MiRBase miRNA analysis with STAR

MiRBase miRNA analysis with STAR 0 Hi All, I am using the latest mice reference genome (GRCm39) for small RNAseq/miRNA-seq analysis. MiRBase database doesn’t have any GFF/GTF file for the mouse mature-miRNA/loop-miRNA. I just have mature-miRNA and loop-miRNA fasta sequences from MiRBase. How I can use the STAR tool to…

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Inquiry related to vcf file and formatting

Hello everyone, I am trying to run predixcan software. But its showing error as segmentation fault implying that there is something wrong with my vcf files. I am sharing the header of vcf file. ##fileformat=VCFv4.1 ##INFO=<ID=LDAF,Number=1,Type=Float,Description=”MLE Allele Frequency Accounting for LD”> ##INFO=<ID=AVGPOST,Number=1,Type=Float,Description=”Average posterior probability from MaCH/Thunder”> ##INFO=<ID=RSQ,Number=1,Type=Float,Description=”Genotype imputation quality from…

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microarray miRNA expression data analysis

I wrote a script on how to analyze the microarray-based miRNA expression data. Here is my code: # general config baseDir <- ‘.’ annotfile <- ‘mirbase_genelist.tsv’ setwd(baseDir) options(scipen = 99) require(limma) # read in the data targets <- read.csv(“/media/mdrcubuntu/46B85615B8560439/microarray_text_files/targets.txt”, sep=””) # retain information about background via gIsWellAboveBG project <- read.maimages(targets,source=”agilent.median”,green.only…

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