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Published 20 hours ago • verified publisher icon bcgsc

How to remove the isoform in the trasncript.fa file?

Open mathavanpu opened this issue 3 years ago • 3 comments

Hello , I am doing the denvo transcriptome assembly, please guide me how to remove the isoforms in the transcript.fa file, The output of transcript.fa file has transcript start as E1,E2, E3. what does it mean?

Please report

  • [ ] version of RNA-Bloom with java -jar RNA-Bloom.jar -version

  • [ ] RNA-Bloom v1.3.1

  • [ ] version of java with java -version

  • [ ] openjdk version "1.8.0_265"

  • [ ] exact command used to run RNA-Bloom

  • [ ] transcript.fa

mathavanpu avatar Dec 15 '21 06:12 mathavanpu

The transcripts in transcripts.fa are assembled based on extensions of seed fragments, which were reconstructed during the 2nd stage of the assembly. These fragments were split into different coverage strata. The E1, E2, and E3 prefixes correspond to 10^1, 10^2, and 10^3, respectively.

What are you trying to remove?

kmnip avatar Dec 15 '21 22:12 kmnip

Hello, Thank you very much for the reply Please tell me remove the isoforms in the trasncript.fa file

mathavanpu avatar Dec 16 '21 05:12 mathavanpu

I recommend using EvidentialGene: http://arthropods.eugenes.org/EvidentialGene/about/EvidentialGene_trassembly_pipe.html

Also, refer to their preprint here: https://www.biorxiv.org/content/10.1101/829184v1.full

kmnip avatar Dec 16 '21 07:12 kmnip