Need to reverse seq of read in Fastq2 (Illummia) for alignment

[Votinhkiem90]

Hi everyone!
Present, I have two file *fastq (fastq_1 and fastq_2) of Illumina.
follow me known: file fastq_1 is seq from 3' - 5', and fastq_2 is seq form 5' - 3'. So when I want to align between two file. Need to reverse reads of fastq_2? or the seq of fastq_2 was reversed automatically by Illumina?
What should i do?
Thanks for help.

[dpryan]

They're both 5'->3' (nucleic acid sequences always are) and you don't need to reverse complement anything, just let the aligner deal with that.

[lindenb]

Ryan is right. As far as I know you only have to do this for mate-paired sequencing.

[Votinhkiem90]

Ryan is right. As far as I know you only have to do this for mate-paired sequencing.

Thanks to help. Yesterday, I sent an email to technical Illumina and they were reply same Dryan cmt.