Will I able to run Cogent on RNAspades output?

[maorkn]

I've run Cogent on my iso-seq run and got really got results. short illumina reads map to it at ~65% alignment and I get a busco completeness score of 65% with very little duplicates. I've, using hisat2, take the unaligned reads from several libraries and constructed a transcriptome using RNAspades. the output gets me to a busco completeness score of 97% but there are many duplicates (45%). I want to use cogent on the transcripts from spades to form coding families similar to what I've done with the iso-seq output. should there be any problem doing this? is there something I'm missing?

[Magdoll]

hi @maorkn ,

I think that idea should work! taking unaligned short reads to assemble is a great idea too. Please try Cogent and let me know how it goes.
-Liz

[maorkn]

Hi! I've actually done it already and it seemed to work great! Any thoughts on how to evaluate the assembly? Busco on transcriptome mode gives poor scores although the reads algin well.

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On Sat, 11 Apr 2020, 06:05 Elizabeth Tseng, ***@***.***> wrote: hi @maorkn <https://github.com/maorkn> , I think that idea should work! taking unaligned short reads to assemble is a great idea too. Please try Cogent and let me know how it goes. -Liz — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#81 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEUBXQIACG425EKTRMWEFQLRL7M6VANCNFSM4LVUJ7XQ> .