order of read1.fastq read2.fastq (or read2.fastq read1.fastq)

[Peter Sudmant]

What is the expected outcome of mapping paired end reads from a read1.fq and read2.fq file, both properly ordered, but passing in read1.fq read2.fq versus read2.fq read1.fq? I seem to be getting no problems with fastq2 fastq1 confuses me a bit...?

Thanks very much!

[Mike]

Similar question: https://groups.google.com/forum/#!searchin/rna-star/cufflinks/rna-star/2UQa1Cxs_bQ/_O5tFiBjL0kJ


For my stranded RNA-seq I always do read2.fq first because if I put read1.fq first the strands are all opposite of what they're supposed to be in the output .sam file.  I've tried "read1.fq read2.fq" and "read2.fq read1.fq" and that's the only difference I've seen.

[Peter Sudmant]

Thank you, the link to the similar question answers my question perfectly. 

Thank you!