Hi everyone,
For a while now I have been working on my de novo Trinity assembly (fish species). Using my de novo transcriptome I have been able to do some interesting differential expression analyses. Then the genome-guided option of Trinity was launched and I tried it using the second version of our draft genome. I didn't use the first genome version as some of my genes of interest were poorly (wrong) assembled and also, on occasion, partially within gaps. Now this is mostly corrected and I hoped that doing the genome guided Trinity would reduce the number of transcripts. I went from 320520 'genes' and N50 1235 to 342099 'genes' and N50 1716.
So better N50 but more transcripts... Also, if I do abundance estimation a FPKM cutoff of 2 for the first gives ~30 000 'genes' and the second ~119 000 'genes'.
Based on stats only - which would you chose to use for DE analysis? Considering redoing Trinotate and all DE analyses with the genome guided version.
Any thoughts are most welcome
For a while now I have been working on my de novo Trinity assembly (fish species). Using my de novo transcriptome I have been able to do some interesting differential expression analyses. Then the genome-guided option of Trinity was launched and I tried it using the second version of our draft genome. I didn't use the first genome version as some of my genes of interest were poorly (wrong) assembled and also, on occasion, partially within gaps. Now this is mostly corrected and I hoped that doing the genome guided Trinity would reduce the number of transcripts. I went from 320520 'genes' and N50 1235 to 342099 'genes' and N50 1716.
So better N50 but more transcripts... Also, if I do abundance estimation a FPKM cutoff of 2 for the first gives ~30 000 'genes' and the second ~119 000 'genes'.
Based on stats only - which would you chose to use for DE analysis? Considering redoing Trinotate and all DE analyses with the genome guided version.
Any thoughts are most welcome
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