Adapters trimming for BGI-seq?

[uzi_maruzi]

Hi everyone,

Recently I just received PEreads from BGI-seq, and the sequencer company provide me with this adapters index:
No code has to be inserted here........etc.....

So, I used those shrt sequences to trim my reads using trimmomatic in Galaxy, and prepared the fasta seq as follow for trimming:

>index1/1
GGTCCATT
>index1/2
TTAGGTAG
>index2/1
GGTCCATT
>index2/2
GGTCACTA
>index3/1
GGTCCATT
>index3/2
TCCGCACT
...etc...

Did I use the information correctly? because recently I just found that others have been using:
forward_adapter = "AAGTCGGAGGCCAAGCGGTCTTAGGAAGACAA"
reverse_adapter = "AAGTCGGATCGTAGCCATGTCGTTCTGTGAGCCAAGGAGTTG"

to trim the adapters, not sure if its for SE only or also PE. Thank you