Question: salmon output files in Galaxy
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keren.maor • 40 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
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modified 5 months ago
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Jennifer Hillman Jackson ♦ 25k
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5 months ago by
keren.maor • 40
