Hi all,
I just got to know about the paired-end short reads sequencing. Can someone help me clarify if i have understood it correctly?
From what i understand, in one sheared genomic fragment, (eg 5'AdaptorTTTTTTT..........CCCCCCC3' and 5' adaptor GGGGGG.........AAAAAAA), only 35bp can be read from both ends.
Does that includes the adaptor sequence? i.e (5'Adaptor sequence +TTTT...til it makes up to 35bp) and 5'AdaptorGGGGG.. for complementary sequence read.
Thus based on these short fragments they are aligned and there may be unknown sequences between the two adaptors.
Suppose if i want find a promoter region of a GOI, what I can do is to BLAST my GOI and find an adaptor sequence that is in my GOI region and another outside of the gene in the 5'UTR?
From there I design primers to amplify the region I want (eg 5'TTTTTT and 5'GGGGGG if I take the above mentioned gene sequence as an example?)
Please correct me if i have misuderstood the technology. Thanks heaps.
I just got to know about the paired-end short reads sequencing. Can someone help me clarify if i have understood it correctly?
From what i understand, in one sheared genomic fragment, (eg 5'AdaptorTTTTTTT..........CCCCCCC3' and 5' adaptor GGGGGG.........AAAAAAA), only 35bp can be read from both ends.
Does that includes the adaptor sequence? i.e (5'Adaptor sequence +TTTT...til it makes up to 35bp) and 5'AdaptorGGGGG.. for complementary sequence read.
Thus based on these short fragments they are aligned and there may be unknown sequences between the two adaptors.
Suppose if i want find a promoter region of a GOI, what I can do is to BLAST my GOI and find an adaptor sequence that is in my GOI region and another outside of the gene in the 5'UTR?
From there I design primers to amplify the region I want (eg 5'TTTTTT and 5'GGGGGG if I take the above mentioned gene sequence as an example?)
Please correct me if i have misuderstood the technology. Thanks heaps.
Comment