de-novo transcript assembly using genome-guided bam

gpertea / stringtie

Transcript assembly and quantification for RNA-Seq

MIT License

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de-novo transcript assembly using genome-guided bam #316

Open ARW-UBT opened 3 years ago

ARW-UBT commented 3 years ago

Hi, I read about StringTie and I am wondering whether it could be used to de-novo assemble a transcriptome from RNA-Seq data using a genome of a closely related species (annelids) as a guide? But I was not able to identify the step in the StringTie workflow, where I can get transcripts (as fasta?). Is it after the merge step #3 as described in https://ccb.jhu.edu/software/stringtie/index.shtml?t=manual#input?

Best regards

JC-therea commented 2 years ago

I am having the same issue. I am doing a saturation analysis subsampling a bam file and when I use RNA-seq data with 4,680,970 reads it seems that there are not enough reads and Stringtie crashes. When I use more reads the program works fine.

PD: I am working on S. pombe's genome