stringtie/2.0.3 ignoring reads

[zhezhenwang]

I am working with stringtie/2.0.3 and have 2 questions regarding this tool. Q1: Is it better merge bam files first and then run stringtie or run stringtie for each sample and then stringtie merge I did observe different results

Q2 I used stringtie WT.bam -p 8 --rf -A -C -c 0.001 -s 0.001 -t -m 50 just to get all transcripts possible and got the following The reads are all (-) strand but on the left where there is very few reads there is several transcripts called while in the middle only one transcript on the (+) strand is called, but the transcript on the (-) strand is the one we are interested