text: user4469: I am running some analysis on an RNA-seq dataset. I have a list of transcripts that are potential lncRNA for which I ran both Kallisto and Salmon aligners. The input data for index building and quantification includes mRNA as well as these potential lncRNA.
  Commands for one replicate: 
  Salmon
  salmon index --keepDuplicates -t transcripts.fasta -i index_directory/ -k 31
  salmon quant --seqBias --gcBias -i index_directory/ --libType ISR --auxDir index_directory/ -1 sample_R1.fastq.gz -2 sample_R2.fastq.gz -o output_name
  
  Kallisto
  kallisto index -i kallisto_index.idx transcripts.fasta
  kallisto quant -i kallisto_index.idx -o output_name --rf-stranded sample_R1.fastq.gz sample_R2.fastq.gz
  
  Then I used the tpm values, averaged replicates (3) and plotted the number of transcripts per condition that had a tpm > 2. Same result for tpm > 5.
  The following graph shows the for mRNA:
  
  And for lncRNA:
  
  Again, the analysis were done with both lncRNA and mRNA transcripts together in the same fasta file.
  The overlap is not shown here but is always smaller than the count for Kallisto, for the lncRNA.
  In literature both tools seem to have similar results. I cannot find a reason for this. If there would be an error somewhere I would expect to see also differences in the conding RNAs which does not happen.
  
  user4575: There has been a detailed comparison of kallisto and salmon for lncRNA transcripts by Zheng et al https://www.biorxiv.org/content/biorxiv/early/2018/01/09/241869.full.pdf
  It shows them to be near identical. This suggests there is some problem with the way you made the comparison/plot.
  
original_text: 4469: <p>I am running some analysis on an RNA-seq dataset. I have a list of transcripts that are potential lncRNA for which I ran both Kallisto and Salmon aligners. The input data for index building and quantification includes mRNA as well as these potential lncRNA.</p>
  
  <p>Commands for one replicate: </p>
  
  <p>Salmon</p>
  
  <pre><code>salmon index --keepDuplicates -t transcripts.fasta -i index_directory/ -k 31
  salmon quant --seqBias --gcBias -i index_directory/ --libType ISR --auxDir index_directory/ -1 sample_R1.fastq.gz -2 sample_R2.fastq.gz -o output_name
  </code></pre>
  
  <p>Kallisto</p>
  
  <pre><code>kallisto index -i kallisto_index.idx transcripts.fasta
  kallisto quant -i kallisto_index.idx -o output_name --rf-stranded sample_R1.fastq.gz sample_R2.fastq.gz
  </code></pre>
  
  <p>Then I used the tpm values, averaged replicates (3) and plotted the number of transcripts per condition that had a tpm > 2. Same result for tpm > 5.</p>
  
  <p>The following graph shows the for mRNA:</p>
  
  <p><a href="https://i.stack.imgur.com/dGJhe.jpg" rel="noreferrer"><img src="https://i.stack.imgur.com/dGJhe.jpg" alt="enter image description here"></a></p>
  
  <p>And for lncRNA:</p>
  
  <p><a href="https://i.stack.imgur.com/ZC3CA.jpg" rel="noreferrer"><img src="https://i.stack.imgur.com/ZC3CA.jpg" alt="enter image description here"></a></p>
  
  <p>Again, the analysis were done with both lncRNA and mRNA transcripts together in the same fasta file.</p>
  
  <p>The overlap is not shown here but is always smaller than the count for Kallisto, for the lncRNA.</p>
  
  <p>In literature both tools seem to have similar results. I cannot find a reason for this. If there would be an error somewhere I would expect to see also differences in the conding RNAs which does not happen.</p>
   4575: <p>There has been a detailed comparison of kallisto and salmon for lncRNA transcripts by Zheng et al <a href="https://www.biorxiv.org/content/biorxiv/early/2018/01/09/241869.full.pdf" rel="nofollow noreferrer">https://www.biorxiv.org/content/biorxiv/early/2018/01/09/241869.full.pdf</a></p>
  
  <p>It shows them to be near identical. This suggests there is some problem with the way you made the comparison/plot.</p>
  