Answers.Body: <p>I have heard that the <a href="http://srna-workbench.cmp.uea.ac.uk/" rel="nofollow noreferrer">Small RNA Workbench</a> from UEA can be an easy solution for a full small RNA pipeline.  It is java based, has a GUI, and is supposed to be easy to install and run.  I am not an expert in small RNA analysis, but I think this pipeline will certainly given you an idea about the steps needed for a small RNA analysis, it has been put together by experts.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-11-20T11:20:34.313Z
Answers.Text: Thanks a lot! I think that can be a good starting point. Also, probably I can get some help from the authors.... fingers crossed!
Answers.UserDisplayName: FJ_Bioinf
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-11-19T07:34:22.610Z
Answers.LastActivityDate: 2019-11-19T07:34:22.610Z
Answers.UserDisplayName: Jay Moore
Answers.Body: <p>piPipes is biased for piRNAs but should be a good starting point:</p>
  
  <p><a href="https://github.com/bowhan/piPipes/wiki/smallRNA-seq" rel="nofollow noreferrer">https://github.com/bowhan/piPipes/wiki/smallRNA-seq</a></p>
  
  <p>Well documented and with many features.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-04-17T19:27:53.277Z
Answers.LastActivityDate: 2020-04-17T19:27:53.277Z
Answers.UserDisplayName: fridaymeetssunday
Answers.Body: <p>Check <a href="https://nf-co.re/" rel="nofollow noreferrer">nf-core</a> for all the pipelines they have, including <a href="https://nf-co.re/smrnaseq" rel="nofollow noreferrer">small-RNA seq</a>. To run them, you have to use <a href="https://nextflow.io/" rel="nofollow noreferrer">Nextflow</a>.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-10-11T09:31:39.667Z
Answers.LastActivityDate: 2021-10-11T09:31:39.667Z
Answers.UserDisplayName: user324810
Answers.Body: <p>As far as I'm concerned, bowtie 1 is still the method of choice since it rather mature and fast. </p>
  
  <p>And yes, pseudoaligner such as salmon are probably not the best choice For once, they need a reference "transcriptome", which is usually available for RNA-Seq but not so much for small-RNAs. Also the way they handle multiple mapping locations is probably not ideal for small-RNAs that may have excessive number mapping location.</p>
  
  <p>I've also written a simple <a href="https://github.com/seb-mueller/snakemake_sRNAseq" rel="nofollow noreferrer">snakemake-pipeline</a> which simply performs some standard pre-processing and mapping against a reference genome along with QC and coverage tracks. It's still work in progress, but I'd be curious about any feedback.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-05-18T08:02:43.107Z
Answers.LastActivityDate: 2020-05-18T08:02:43.107Z
Answers.UserDisplayName: Sebastian Müller
Body: <p>I am a newbie in this world (just finished my master's on bioinformatics. As a practice, a researcher gave me 4 fastq files from a small RNAseq experiment, to see if I am able to reproduce their results but with an updated pipeline and tools (they used bowtie in 2014). 
  I used fastqc for the quality check and I removed the adapters properly. </p>
  
  <p>My first intention was to use Salmon for pseudo-align them, but after do some reading it seems not to be a good idea for such small RNAs. </p>
  
  <p>Can anyone provide me with some light on this? Which alignment tool use and which parameters, and etc. Ideally a proper protocol/pipeline would be amazing. </p>
  
  <p>Thank you in advance...</p>
  
  <p>PD: I was thinking to use the HISAT2 with the full genome (or the pre-builded index from HISAT2 website). </p>
  
  <p>Kind regards, 
  and thank you in advance!</p>
  
Tags: <trna>
Title: Pipeline to analyse small RNAseq and tRNAs?
ThreadText: # Pipeline to analyse small RNAseq and tRNAs?
  
  (Asked by: username_0 on 2019-11-18)
  
  I am a newbie in this world (just finished my master's on bioinformatics. As a practice, a researcher gave me 4 fastq files from a small RNAseq experiment, to see if I am able to reproduce their results but with an updated pipeline and tools (they used bowtie in 2014).
  I used fastqc for the quality check and I removed the adapters properly.
  
  My first intention was to use Salmon for pseudo-align them, but after do some reading it seems not to be a good idea for such small RNAs.
  
  Can anyone provide me with some light on this? Which alignment tool use and which parameters, and etc. Ideally a proper protocol/pipeline would be amazing.
  
  Thank you in advance...
  
  PD: I was thinking to use the HISAT2 with the full genome (or the pre-builded index from HISAT2 website).
  
  Kind regards,
  and thank you in advance!
  
  **Tags:** trna
  
  
  ---
  
  ## 4 answers
  
  ### Answer by username_1 on 2019-11-19. Score: 1
  
  I have heard that the [Small RNA Workbench](http://srna-workbench.cmp.uea.ac.uk/) from UEA can be an easy solution for a full small RNA pipeline. It is java based, has a GUI, and is supposed to be easy to install and run. I am not an expert in small RNA analysis, but I think this pipeline will certainly given you an idea about the steps needed for a small RNA analysis, it has been put together by experts.
  
  > **Comments:**
  > **username_0**: Thanks a lot! I think that can be a good starting point. Also, probably I can get some help from the authors.... fingers crossed!  
  
  ---
  
  ### Answer by username_2 on 2020-04-17. Score: 1
  
  piPipes is biased for piRNAs but should be a good starting point:
  
  <https://github.com/bowhan/piPipes/wiki/smallRNA-seq>
  
  Well documented and with many features.
  
  
  ---
  
  ### Answer by username_3 on 2021-10-11. Score: 1
  
  Check [nf-core](https://nf-co.re/) for all the pipelines they have, including [small-RNA seq](https://nf-co.re/smrnaseq). To run them, you have to use [Nextflow](https://nextflow.io/).
  
  
  ---
  
  ### Answer by username_4 on 2020-05-18. Score: 1
  
  As far as I'm concerned, bowtie 1 is still the method of choice since it rather mature and fast.
  
  And yes, pseudoaligner such as salmon are probably not the best choice For once, they need a reference "transcriptome", which is usually available for RNA-Seq but not so much for small-RNAs. Also the way they handle multiple mapping locations is probably not ideal for small-RNAs that may have excessive number mapping location.
  
  I've also written a simple [snakemake-pipeline](https://github.com/seb-mueller/snakemake_sRNAseq) which simply performs some standard pre-processing and mapping against a reference genome along with QC and coverage tracks. It's still work in progress, but I'd be curious about any feedback.
  
  
  ---
  
  