Shorter forward reads than reverse

[GenoMax]

Yes, reads have been trimmed

Then it is odd that only R1 was trimmed (or trimmed to a larger extent than R2). If you have short inserts (and thus read-through into adapters on other end) then R2 reads should also be trimmed to a similar extent.

You still need to address questions in other comments above.

[DanielSai]

Have the reads been trimmed?

Yes, reads have been trimmed

[kmcarr]

Have the reads been trimmed?

[GenoMax]

There is no logical reason (other than an assymetric run setup mentioned by @nucacidhunter) to get shorter R1 reads compared to R2. What kind of sequencing are you doing and what is the run setup?

[nucacidhunter]

You have not given much details but one reason would be sequencing configuration for example, R1 was set to less cycles than R2.

[DanielSai]

Hello,
I'm DanielSai from Australia.

I did a next gen run on my sample using the illumina miseq machine. I'm getting shorter forward sequence reads than the reverse reads. What could be the problem and how can it rectified in subsequent runs?