Long reads question

[Zoe Ward]

Hi Alex,

I am planning on using stringtie to first assemble 'super.reads' from my paired-end data and then use these as input to STAR along with the unassembled fastq files (manual here: https://ccb.jhu.edu/software/stringtie/index.shtml?t=manual)

The 'super.reads' will be about 300bp long hopefully so I was wondering if I would need to use the STAR long with the 'super.reads' as single (unpaired) reads and STAR for the paired-end fastq files and then merge the two output bam files?

If you think this is the way to go could you advise on parameters for the long protocol?

Zoe.

[Alexander Dobin]

Hi Zoe,

I would first try to map ~300b reads with normal STAR. If it becomes too slow, then you would need to switch to STARlong.

Cheers

Alex