Question: salmon output files in Galaxy
gravatar for keren.maor
5 months ago by
keren.maor40 wrote:

Hi all, I used Salmon tool in Galaxy to both align to my de novo transcriptome assembly and to quantify number of reads per transcript (assembled using Trinity--> Transdecoder). I got two output files per sample, named :" Quantification" and "Gene quantification". I don't understand what is the difference between them as the columns are the same: id, Length EffectiveLength, TPM, NumReads. The ids style is a bit different, for example in the Quantification file :"TRINITY_DN100010_c0_g1::TRINITY_DN100010_c0_g1_i1::g.27078::m.27078" while in the Gene quantification file it is: "TRINITY_DN9997_c0_g1::TRINITY_DN9997_c0_g1_i1::g.341840" Can anyone advice me which one of these I should use? Thank you all

ADD COMMENTlink modified 5 months ago by Jennifer Hillman Jackson25k • written 5 months ago by keren.maor40
gravatar for Jennifer Hillman Jackson
5 months ago by
United States
Jennifer Hillman Jackson25k wrote:


The output represents:

  • Quantification = summaries by transcript
  • Gene Quantification = summaries by gene

Which to use depends on what tools you plan to input the data to and your analysis goals. Please see the Galaxy tutorials here for examples of using these data:

Thanks! Jen, Galaxy team

ADD COMMENTlink written 5 months ago by Jennifer Hillman Jackson25k
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