text: user6515: 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!
  
  user3828: I have heard that the Small RNA Workbench 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.
  
  user108: 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.
  
  user1461: 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 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.
  
  user4413: Check nf-core for all the pipelines they have, including small-RNA seq. To run them, you have to use Nextflow.
  
original_text: 6515: <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>
   3828: <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>
   108: <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>
   1461: <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>
   4413: <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>
  