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broadinstitute / pilon

Pilon is an automated genome assembly improvement and variant detection tool
GNU General Public License v2.0
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pilon for rna-seq #85

Closed manuelsmendoza closed 5 years ago

manuelsmendoza commented 5 years ago

Hi!

I have a question related to #50... I wanna to build a transcriptome of reference (without genome) and to do so I've thought: (1) de novo assembly by Trinity, (2) clustering the transcripts to reduce redundancy using grouper and then (3) make a consensus reference for each cluster using pilon.

Which is your opinion?

cheers, ~MM.

weedcentipede commented 5 years ago

Hi @manuelsmendoza, As a opinion: Right now I'm polishing mtDNA from RNA-seq reads, the problem with this is that numts interfere with the polishing process so..., if you're transcripts are single copy and don't present that many SNPs you could/should try it, but if you have many variants (for whatever reason) be careful...

manuelsmendoza commented 5 years ago

Thanks so much @OnlyHigh! The second scenario is my case... I'm working with hypervariable organisms with many mutations along the genome... Finally, I've written a little script to extract the "consensus" sequence from Grouper.