Difference between read count from Star and stringtie

gpertea / stringtie

Transcript assembly and quantification for RNA-Seq

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Difference between read count from Star and stringtie #415

Open giacuong171 opened 9 months ago

giacuong171 commented 9 months ago

Hello,
I'm working on getting TPM from gene count file of star and checking whether the output is correct or not. I compared the correlation between tpm values of one single exom with single transcript genes. The correlation is around 0,97 but not 1. so i dived more into it with getting read count of gene from prepDe.py of stringtie. But now there is a gene that has only 1 read from star but 600 reads from stringtie and i have no clue how that happened. Does someone might have idea for that ?

giacuong171 commented 9 months ago

i understand that stringtie will firstly try to build a super-reads, but is it the reason why the number of reads is so different?