STAR paired end mode question

Question

[shinyjj]

Hi biostars,

I have two paired end fastq files, ex_R1.fastq and ex_R2.fastq.

1) Can someone help me with finding a command line in STAR to generate a single BAM file with these two fastq files?

2) When there are two paired ends fastq files, does it make sense or possible to combine those two fastq files into one fastq file?

[ATpoint]

Could you please read the manual first which covers these essentials?

https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf