Setting up -pHeterozygosity parameter

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Harish K

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Dec 31, 2022, 3:19:57 PM12/31/22

to EvidentialGene

Hi Dr, Gilbert,

Hope you're doing well. We have sequenced and denovo assembled a few wild type fishes from different sexes and seasons.

Since we generally use Evidentialgene to reduce the over-assembly eariler, I wanted to check if there was any suggestion on setting up the pHeterozygosity parameter. We are assuming that these are tetraploid fishes and there is bound to be some variability since the fishes aren't from the same school.

Regards,

Harish

Don Gilbert

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Dec 31, 2022, 11:16:19 PM12/31/22

to Harish K, EvidentialGene

Harish,

A quick answer from tr2aacds.pl -help

  -pHeterozygosity=[0..9] : reduce percent identities for heterozygous organism sample (default 0),
      this lowers alternate/paralog identity cutoffs and classes, and drops more high-identity transcripts

I suggest you test it (eg -phet 0 vs -phet 3 or 5 or 9),  and if you can measure het. in your fishes, that may help pick a value. 
I don't generally recommend its use unless you know/measure that your RNA sample is notably heterozygous, 
but I've not tested enough to say what.range of heteroz. is significant in affecting this.

- Don

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