Paired End Seq

[papori]

Hi,
i just got rna data from illumina highseq2000.
when i checked the data quality(FASTQC) i found that the first end has higher quality than the second end (by far...)

Any idea why?

Best,
Pap

[pmiguel]

Could be that synthesis of the second strand ("turn around") went poorly for some reason. Or that the SBS reagents started to decline in capability as the days they spent at 4 oC increased.

--
Phillip

[papori]

Could be that synthesis of the second strand ("turn around") went poorly for some reason. Or that the SBS reagents started to decline in capability as the days they spent at 4 oC increased.

--
Phillip

thanks pmiguel !