Adapters sequence for trimming PE reads

[uzi_maruzi]

Hi everyone,

Recently I just received PEreads from BGI-seq, and the sequencer company provide me with this adapters index:

		i7_Index_ID	i7index配列	i5_Index_ID	i5index配列
DNA	Index	i7ID	i7Seq	i5ID	i5Seq
SG-003	M5041/M7091	M7091	CAATCGTT	M5041	CTGCGGAT
SG-015	M5041/M7092	M7092	AGCCATAC	M5041	CTGCGGAT
SG-37	M5041/M7093	M7093	GTGATAGG	M5041	CTGCGGAT
SG-55	M5041/M7094	M7094	TCTGGCCA	M5041	CTGCGGAT
SG-77	M5041/M7101	M7101	TATGAACA	M5041	CTGCGGAT

.......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