output unmapped file in STAR alignment

Question

[linjc.xmu]

Hi All. I am using STAR alignment to remove rRNA reads, and collect unmapped reads for further alignment. My command line is: STAR --genomeDir ./genome/index/rRNA/ --readFilesIn RA1_R1.fastq RA1_R2.fastq --clip3pNbases 12 --clip5pNbases 50 --outFileNamePrefix rRNA1 --outReadsUnmapped Fastx

However, the output unmapped file mix read1 and read2 together, not in a separated R1.fastq and R2.fastq. Does anyone know how to set parameters? Thanks a lot.

[Devon Ryan]

Which version of STAR are you using?

[linjc.xmu]

STAR_2.5.3a, thanks.

[Devon Ryan]

Maybe this is fixed in the latest release (2.6.1a).