gpertea
de-novo transcript assembly using genome-guided bam
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
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
