# \#mirna **URL:** https://help.galaxyproject.org/tag/mirna/119.md [Latest](https://help.galaxyproject.org/latest.md) · [Categories](https://help.galaxyproject.org/categories.md) · [Tags](https://help.galaxyproject.org/tags.md) --- ## [miRNA alignment on Bowtie2/miRDeep](https://help.galaxyproject.org/t/mirna-alignment-on-bowtie2-mirdeep/16494)
**Author:** [@Daghshy](https://help.galaxyproject.org/u/Daghshy)\ **Replies:** 1\ **Last updated:** [November 15, 2025, 1:55am UTC](https://help.galaxyproject.org/t/mirna-alignment-on-bowtie2-mirdeep/16494 "2025-11-15T01:55:24Z")
I was using a public RNA-Seq dataset and was exploring the insights and saw that the miRNA had very low counts compared to the other RNAs and it is logical, I was using STAR with gencode fasta file and gtf files So, I w… --- ## [Running MiRDeep2 with pooled reads from MiRDeep2 Mapper](https://help.galaxyproject.org/t/running-mirdeep2-with-pooled-reads-from-mirdeep2-mapper/16182)
**Author:** [@jrw025](https://help.galaxyproject.org/u/jrw025)\ **Replies:** 4\ **Last updated:** [August 28, 2025, 8:00pm UTC](https://help.galaxyproject.org/t/running-mirdeep2-with-pooled-reads-from-mirdeep2-mapper/16182 "2025-08-28T20:00:44Z")
I’m trying to run MiRDeep2 to identify novel miRNAs from my non-model species. I have successfully mapped my cleaned small RNA reads to my genome using MiRDeep2 Mapper and individually run the resulting collapsed read fi… --- ## [Datasets error and failure in DE analysis for mirna-seq](https://help.galaxyproject.org/t/datasets-error-and-failure-in-de-analysis-for-mirna-seq/14926)
**Author:** [@kmy.88](https://help.galaxyproject.org/u/kmy.88)\ **Replies:** 1\ **Last updated:** [March 5, 2025, 7:06pm UTC](https://help.galaxyproject.org/t/datasets-error-and-failure-in-de-analysis-for-mirna-seq/14926 "2025-03-05T19:06:29Z")
Hi, I;m not sure where’s the problem, but I can’t seem to run differential expression analysis for miRNA-seq. I have a list of miRNAs with read counts of all samples in CSV format. Once uploaded, I opted for RNA-seq (Too… --- ## [Can miRNA differential expression analysis be performed using a mRNA-like pipeline with a GTF file from miRBase?](https://help.galaxyproject.org/t/can-mirna-differential-expression-analysis-be-performed-using-a-mrna-like-pipeline-with-a-gtf-file-from-mirbase/13879)
**Author:** [@Maryam\_Momeni](https://help.galaxyproject.org/u/Maryam_Momeni)\ **Replies:** 2\ **Last updated:** [November 12, 2024, 5:54pm UTC](https://help.galaxyproject.org/t/can-mirna-differential-expression-analysis-be-performed-using-a-mrna-like-pipeline-with-a-gtf-file-from-mirbase/13879 "2024-11-12T17:54:40Z")
I am planning to perform differential expression analysis for the miRNA reads of an RNA-seq dataset that was not produced using deep sequencing. After reading the Whole transcriptome analysis of Arabidopsis thaliana tuto… --- ## [Files for miRNA differential expression analysis](https://help.galaxyproject.org/t/files-for-mirna-differential-expression-analysis/7901)
**Author:** [@LaiaGutierrez](https://help.galaxyproject.org/u/LaiaGutierrez)\ **Replies:** 8\ **Last updated:** [November 12, 2024, 12:08am UTC](https://help.galaxyproject.org/t/files-for-mirna-differential-expression-analysis/7901 "2024-11-12T00:08:37Z")
Hi, I have some files obtained by small non-coding RNA sequencing in humans. My aim is to identify the miRNA and do differential expression. I am following this protocol: Hands-on: miRNA differential expression analysi… --- ## [miRDeep2 output](https://help.galaxyproject.org/t/mirdeep2-output/11031)
**Author:** [@Sabrina\_Napoletano](https://help.galaxyproject.org/u/Sabrina_Napoletano)\ **Replies:** 3\ **Last updated:** [November 8, 2023, 8:35pm UTC](https://help.galaxyproject.org/t/mirdeep2-output/11031 "2023-11-08T20:35:19Z")
Hi I performed quantifier with miRDeep2 and I had this result. Could someone tell me if this result is correct. Thank you --- ## [Identification of novel and known miRNAas using mirdeep2 in galaxy](https://help.galaxyproject.org/t/identification-of-novel-and-known-mirnaas-using-mirdeep2-in-galaxy/11030)
**Author:** [@Alok\_Dubey](https://help.galaxyproject.org/u/Alok_Dubey)\ **Replies:** 1\ **Last updated:** [October 23, 2023, 10:33pm UTC](https://help.galaxyproject.org/t/identification-of-novel-and-known-mirnaas-using-mirdeep2-in-galaxy/11030 "2023-10-23T22:33:30Z")
Hello everyone, Im cureeently working on miRNA data and i need to know the known and novel mirnas present in my samples. im using mirdeep2 for mapping and quantification. Here mirdeep2 is asking input files colapse and … --- ## [EdgeR doesn´t run with count matrix in tabular format (obtained from mirDeep2 Quantifier)](https://help.galaxyproject.org/t/edger-doesn-t-run-with-count-matrix-in-tabular-format-obtained-from-mirdeep2-quantifier/9976)
**Author:** [@alepando018](https://help.galaxyproject.org/u/alepando018)\ **Replies:** 1\ **Last updated:** [May 2, 2023, 6:31pm UTC](https://help.galaxyproject.org/t/edger-doesn-t-run-with-count-matrix-in-tabular-format-obtained-from-mirdeep2-quantifier/9976 "2023-05-02T18:31:11Z")
Hello everyrone, This is my first time using Galaxy. I am currently trying to perform Differntial Expression Analysis with Small RNA Seq data and I am having issues with running EdgeR. I have followed this pipeline: … --- ## [Where to get precursor, mature, star miRNA for (MiRDeep2 Quantifier)](https://help.galaxyproject.org/t/where-to-get-precursor-mature-star-mirna-for-mirdeep2-quantifier/9068)
**Author:** [@alio](https://help.galaxyproject.org/u/alio)\ **Replies:** 1\ **Last updated:** [November 23, 2022, 10:11am UTC](https://help.galaxyproject.org/t/where-to-get-precursor-mature-star-mirna-for-mirdeep2-quantifier/9068 "2022-11-23T10:11:47Z")
Hi, Currently working with this workflow tutorial to quantify my sequencing data against the provided A.Thaliana reference. Does zenodo provide more precursor, mature, star miRNA files for other organisms? What other so… --- ## [How to run miRNA analysis to identify miRNAs and for differential expression?](https://help.galaxyproject.org/t/how-to-run-mirna-analysis-to-identify-mirnas-and-for-differential-expression/8777)
**Author:** [@alio](https://help.galaxyproject.org/u/alio)\ **Replies:** 3\ **Last updated:** [October 12, 2022, 8:40pm UTC](https://help.galaxyproject.org/t/how-to-run-mirna-analysis-to-identify-mirnas-and-for-differential-expression/8777 "2022-10-12T20:40:27Z")
Currently using this tutorial as I am working with Arabidopsis Thaliana. I would assume the uploaded files of mature\_miRNA , star\_miRNA , and miRNA\_stem-loop are all specific to A.Thaliana so no change is needed there. I… --- ## [DESeq2 with HISAT2 output?](https://help.galaxyproject.org/t/deseq2-with-hisat2-output/7921)
**Author:** [@LaiaGutierrez](https://help.galaxyproject.org/u/LaiaGutierrez)\ **Replies:** 10\ **Last updated:** [April 29, 2022, 10:48pm UTC](https://help.galaxyproject.org/t/deseq2-with-hisat2-output/7921 "2022-04-29T22:48:15Z")
Hi everybody :slight\_smile: I am working with smallRNA. I followed this protocol (Differential abundance testing of small RNAs). My aim is to do differential expression analysis of siRNA and piRNA using DESeq2. In this… --- ## [Is there a protocol for miRNA Sequencing?](https://help.galaxyproject.org/t/is-there-a-protocol-for-mirna-sequencing/7363)
**Author:** [@LaiaGutierrez](https://help.galaxyproject.org/u/LaiaGutierrez)\ **Replies:** 3\ **Last updated:** [January 25, 2022, 12:29pm UTC](https://help.galaxyproject.org/t/is-there-a-protocol-for-mirna-sequencing/7363 "2022-01-25T12:29:30Z")
Hi, :smile: I am sequencing miRNA and other small RNA. I found a protocol to obtain the counts for smallRNA. However, this involves getting rid of miRNAs. I wanted to know if there is another protocol to obtain the miRN… --- ## [Deduplication for miRNA analysis](https://help.galaxyproject.org/t/deduplication-for-mirna-analysis/6698)
**Author:** [@amir](https://help.galaxyproject.org/u/amir)\ **Replies:** 4\ **Last updated:** [September 27, 2021, 10:52am UTC](https://help.galaxyproject.org/t/deduplication-for-mirna-analysis/6698 "2021-09-27T10:52:06Z")
Hello What is the best tool for deduplication for my data? lets say i have more than 50% duplication in my reads, how should i remove them. I saw some tool but im not sure which one is best for my analysis. Thanks --- ## [miRNA target prediction](https://help.galaxyproject.org/t/mirna-target-prediction/6617)
**Author:** [@CARLOS\_LIZAMA](https://help.galaxyproject.org/u/CARLOS_LIZAMA)\ **Replies:** 1\ **Last updated:** [September 3, 2021, 9:24am UTC](https://help.galaxyproject.org/t/mirna-target-prediction/6617 "2021-09-03T09:24:08Z")
I’m trying to do miRNa target prediction and I was wondering is useful tool to do it, I was using the (http://mirdb.org/), but i dont like too much the output files. Thanks --- ## [miRNA featureCounts](https://help.galaxyproject.org/t/mirna-featurecounts/5761)
**Author:** [@andres2r89](https://help.galaxyproject.org/u/andres2r89)\ **Replies:** 1\ **Last updated:** [April 15, 2021, 10:48am UTC](https://help.galaxyproject.org/t/mirna-featurecounts/5761 "2021-04-15T10:48:43Z")
Hello everyone I am working in Galaxy with miRNAs data. I am trying to pass my reads mapped with Bowtie to counts with the featureCounts app. I have not been successful, the process gives me an error because the miRBa… --- ## [MiRDeep2 identification of novel and known miRNAs](https://help.galaxyproject.org/t/mirdeep2-identification-of-novel-and-known-mirnas/2036)
**Author:** [@amir](https://help.galaxyproject.org/u/amir)\ **Replies:** 28\ **Last updated:** [May 19, 2020, 7:18am UTC](https://help.galaxyproject.org/t/mirdeep2-identification-of-novel-and-known-mirnas/2036 "2020-05-19T07:18:33Z")
Hi After i done Mirdeep2 mapper and quantifier, in Mirdeep2 identifier i got an error which i think the genome was the problem. what should i put i that box. I tried Hg38 human transcriptome but it does not solve the pr… --- ## [Fasta format genome file in mirdeep2 (custom genome)](https://help.galaxyproject.org/t/fasta-format-genome-file-in-mirdeep2-custom-genome/1268)
**Author:** [@maham\_hamid](https://help.galaxyproject.org/u/maham_hamid)\ **Replies:** 3\ **Last updated:** [September 4, 2019, 6:05pm UTC](https://help.galaxyproject.org/t/fasta-format-genome-file-in-mirdeep2-custom-genome/1268 "2019-09-04T18:05:06Z")
I’m using mirdeep2 for analysis of human miRNA data and in this tool, the input requirements of this tool is 2 files from mirdeep2 quantifier, mature.fa and precursor.fa from mirBase and a coresponding genome fasta file. … --- ## [identify MiRNAs(microRNAs) in RNA seq](https://help.galaxyproject.org/t/identify-mirnas-micrornas-in-rna-seq/1277)
**Author:** [@amir](https://help.galaxyproject.org/u/amir)\ **Replies:** 1\ **Last updated:** [May 13, 2019, 9:53pm UTC](https://help.galaxyproject.org/t/identify-mirnas-micrornas-in-rna-seq/1277 "2019-05-13T21:53:49Z")
i want to identify and seprate miRNAs from my Transcript ID list. how should i do that? is there an way in galaxy to Do anything with MicroRNAs. and if i want to seperate and identifis those how my workflow should be .??…