Stringtie --merge with PE and SE files

Question

[marina.v.yurieva]

I'm trying to create a merged gtf from TCGA bam files with Stringtie --merge. But some of the files use SE reads and some - PE reads. Are those bam file compatible and can be used together to generate a new gtf? I tried to find this info in the manual and online but couldn't.

Thank you!

[Kevin Blighe]

How is it that some are single- while others paired-end? I had assumed that TCGA data was almost exclusively paired end. Have you tried to run the command?

[marina.v.yurieva]

Most of the data there is PE but there are some samples that are SE. Some of them are even from the same individuals, it's weird. I'm trying to compare tumor to normal tissue from the same individual and there are few of them with PE and SE reads samples as different biological samples. Read lengths also vary so I don't even know if it would make sense to use samples from the same person with different read lengths or PE and SE but I was wondering if I can combine all of them in one gtf. I haven't tried running it but it will probably work, would it be correct to combine SE and PE bams though?

[Kevin Blighe]

I see. Most of them should be PE, though, right? Can you achieve a large sample n with just the PE samples? I processed both SE and PE RNA-seq samples in the past with no apparent technical / batch effects.