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.

On Sat, 11 Apr 2020, 06:05 Elizabeth Tseng, [email protected] 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 https://github.com/Magdoll/Cogent/issues/81#issuecomment-612308460, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEUBXQIACG425EKTRMWEFQLRL7M6VANCNFSM4LVUJ7XQ .