Open dudududu12138 opened 5 months ago
Hi, I recently ran stringtie2 to assemble transcript from long RNA-seq data. My data is a HIFI cDNA data. And I map raw data to GRCh38 with minimap2. Then I ran stringtie2 with the following code:
stringtie -L -G ref.anno.gtf -o result.gtf alignment.bam
While I noticed that the output result of the gtf file is odd. The min coverage of every transcript is 1 ,while the min coverage of some exons are 0.
Example1 : the transcript has 2 exons , one of them has a 0 coverage
Example2：this is many transcripts with coverage=1, while these are all single-exon transcripts, are them true transcripts?
Thanks!
Hi, I recently ran stringtie2 to assemble transcript from long RNA-seq data. My data is a HIFI cDNA data. And I map raw data to GRCh38 with minimap2. Then I ran stringtie2 with the following code:
While I noticed that the output result of the gtf file is odd. The min coverage of every transcript is 1 ,while the min coverage of some exons are 0.
My question is : How are exons with 0 coverage detected?
Example1 : the transcript has 2 exons , one of them has a 0 coverage
Example2：this is many transcripts with coverage=1, while these are all single-exon transcripts, are them true transcripts?
Thanks!