Answers.Body: <p><em>Answer from @supertech, converted from comment:</em></p>
  <p>This can be frustrating I understand. In my experience it's easier to read the paper and install the modern versions of the tools compatible with your computer (paper was published in 2014). Even more convenient you could open a free account at <a href="https://galaxyproject.org/support/account-quotas/" rel="nofollow noreferrer">https://galaxyproject.org/support/account-quotas/</a> (gives 250GB free space), and do your analysis there. Tophat aligner can be very slow. STAR is better from mapping accuracy to speed; I would recommend that you use that if possible. If you are doing  analysis with large genomes your laptop computer is unlikely to have necessary RAM to run the aligners.</p>
  <ul>
  <li>Answer from @m, converted from comment:*</li>
  </ul>
  <p>Why not then simply use Bioconductor microRNA, which is under active/recent development?</p>
  <p>Looks like STAR has been used for microRNA mapping for ENCODE:</p>
  <p><a href="https://www.encodeproject.org/microrna/microrna-seq/" rel="nofollow noreferrer">https://www.encodeproject.org/microrna/microrna-seq/</a></p>
  <p><em>From the ENCODE pipeline developer (@user3274289):</em></p>
  <p>The ENCODE microRNA pipeline uses STAR for mapping and quantification and should be runnable on mac (you might need one on the beefier side though to have enough memory but i have run some workflows on a new macbook pro). We do not have drosophila STAR index available so you need to generate that using the workflow that is provided. See instructions on github.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-02-13T21:40:35.603Z
Answers.LastActivityDate: 2022-03-17T20:06:15.763Z
Answers.LastEditDate: 2022-03-17T20:06:15.763Z
Answers.UserDisplayName: gringer
Body: <p>I am involved in a Drosophila transcriptomics project in which we have RNAseq data for small RNAs (for microRNAs) in addition to total RNA (for mRNAs).</p>
  <ul>
  <li>The total RNA reads have been analysed satisfactorily using the <a href="https://www.nature.com/articles/nprot.2012.016.pdf" rel="nofollow noreferrer">Tuxedo pipeline</a> using TopHat, Cufflinks, Cuffquant and Cuffdiff. (I run this locally on a fast desktop Mac.)</li>
  <li>Initially we applied the Tuxedo pipeline to the short RNA reads, but abandoned this because of an incidence (1 in 10) of anomalously low or high replicates that was inconsistent with the bigwig plots from the bam stage, displayed in the UCSC browser.</li>
  <li>We there switched to analysing the short RNA reads using the <a href="https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-15-423" rel="nofollow noreferrer">CAP-miRSeq pipeline</a> on Unix, which initially — though very slow — gave consistent results. However recent attempts to process later samples by this method failed as the pipeline can no longer find some dependencies it requires.</li>
  </ul>
  <p>I see no point in spending further time on either of these methods.</p>
  <p><strong>Question</strong></p>
  <p>Has anyone <em>experience</em> of a <em>more modern</em> analysis method for microRNA RNAseq data, preferably one that would run on MacOS?</p>
  <p>I have no trouble in running the Tuxedo pipeline and get good results with total RNA. The problem there is not my computer. Unless someone who has analysed microRNA using this package understands the problem I have encountered, there is no rationale basis for trying this again. As regards Cap-miRSeq, it does not run on the Mac, only on Unix. A colleague set it up on a virtual box. We are our support. Is there anyone working on RNAseq of microRNA?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-02-13T19:21:33.420Z
Comments.Text: Okay, thanks why not then simply use Bioconductor microRNA, which is under active/recent development?
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-02-13T19:42:57.773Z
Comments.Text: @M__  Thanks. Didn’t know about that. I’ll have a look at it.
Comments.UserDisplayName: David
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-02-14T13:10:37.650Z
Comments.Text: @M__ I had a look at it. It seems to be a tool for identifying microRNAs. However that is not the problem. The reference database for the Drosophila genome includes the microRNAs.
Comments.UserDisplayName: David
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-02-14T13:55:50.487Z
Comments.Text: Okay thanks, @llrs will know how to do this, but really I think you are into R-based coding. Between Bioconductor and Seurat there must be a replica of your original program
Comments.UserDisplayName: M__
Tags: <rna-seq><transcriptome>
Title: Alternatives to CAP-miRSeq for microRNA processing
ThreadText: # Alternatives to CAP-miRSeq for microRNA processing
  
  (Asked by: username_0 on 2021-10-04)
  
  I am involved in a Drosophila transcriptomics project in which we have RNAseq data for small RNAs (for microRNAs) in addition to total RNA (for mRNAs).
  
  * The total RNA reads have been analysed satisfactorily using the [Tuxedo pipeline](https://www.nature.com/articles/nprot.2012.016.pdf) using TopHat, Cufflinks, Cuffquant and Cuffdiff. (I run this locally on a fast desktop Mac.)
  * Initially we applied the Tuxedo pipeline to the short RNA reads, but abandoned this because of an incidence (1 in 10) of anomalously low or high replicates that was inconsistent with the bigwig plots from the bam stage, displayed in the UCSC browser.
  * We there switched to analysing the short RNA reads using the [CAP-miRSeq pipeline](https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-15-423) on Unix, which initially — though very slow — gave consistent results. However recent attempts to process later samples by this method failed as the pipeline can no longer find some dependencies it requires.
  
  I see no point in spending further time on either of these methods.
  
  **Question**
  
  Has anyone *experience* of a *more modern* analysis method for microRNA RNAseq data, preferably one that would run on MacOS?
  
  I have no trouble in running the Tuxedo pipeline and get good results with total RNA. The problem there is not my computer. Unless someone who has analysed microRNA using this package understands the problem I have encountered, there is no rationale basis for trying this again. As regards Cap-miRSeq, it does not run on the Mac, only on Unix. A colleague set it up on a virtual box. We are our support. Is there anyone working on RNAseq of microRNA?
  
  **Tags:** rna-seq, transcriptome
  
  > **Comments:**
  > **username_1**: Okay, thanks why not then simply use Bioconductor microRNA, which is under active/recent development?  
  > **username_0**: @username_1  Thanks. Didn’t know about that. I’ll have a look at it.  
  > **username_0**: @username_1 I had a look at it. It seems to be a tool for identifying microRNAs. However that is not the problem. The reference database for the Drosophila genome includes the microRNAs.  
  > **username_1**: Okay thanks, @llrs will know how to do this, but really I think you are into R-based coding. Between Bioconductor and Seurat there must be a replica of your original program  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2022-02-13. Score: 1
  
  *Answer from @supertech, converted from comment:*
  
  This can be frustrating I understand. In my experience it's easier to read the paper and install the modern versions of the tools compatible with your computer (paper was published in 2014). Even more convenient you could open a free account at <https://galaxyproject.org/support/account-quotas/> (gives 250GB free space), and do your analysis there. Tophat aligner can be very slow. STAR is better from mapping accuracy to speed; I would recommend that you use that if possible. If you are doing analysis with large genomes your laptop computer is unlikely to have necessary RAM to run the aligners.
  
  * Answer from @m, converted from comment:\*
  
  Why not then simply use Bioconductor microRNA, which is under active/recent development?
  
  Looks like STAR has been used for microRNA mapping for ENCODE:
  
  <https://www.encodeproject.org/microrna/microrna-seq/>
  
  *From the ENCODE pipeline developer (@user3274289):*
  
  The ENCODE microRNA pipeline uses STAR for mapping and quantification and should be runnable on mac (you might need one on the beefier side though to have enough memory but i have run some workflows on a new macbook pro). We do not have drosophila STAR index available so you need to generate that using the workflow that is provided. See instructions on github.
  
  
  ---
  
  