Hi,
This is a simple question, but I cant find mention of whether or not to routinely trim adapter sequences from Agilent's SureSelect PE library prep kits.
Do any of you routinely apply an adapter trim to your SureSelect samples prior to alignment as part of an existing pipeline?
I have a well defined process for adapter trimming Haloplex FASTQs as there is usually a fair bit of adapter read-through since the amplicons are often shorter than the 2x150bp PE reads that we run.
For SureSelect I wanted to instigate a routine adapter trim as part of an automated pipeline, if for example the genomic DNA had been over-sheared, leading to smaller than ideal fragments, which would result in adapter readthrough (in the same way that I currently have to deal with read-through in Haloplex assays).
Does anyone do this for SureSelect, and if so, what are the adapter sequences that you use?
Thanks
This is a simple question, but I cant find mention of whether or not to routinely trim adapter sequences from Agilent's SureSelect PE library prep kits.
Do any of you routinely apply an adapter trim to your SureSelect samples prior to alignment as part of an existing pipeline?
I have a well defined process for adapter trimming Haloplex FASTQs as there is usually a fair bit of adapter read-through since the amplicons are often shorter than the 2x150bp PE reads that we run.
For SureSelect I wanted to instigate a routine adapter trim as part of an automated pipeline, if for example the genomic DNA had been over-sheared, leading to smaller than ideal fragments, which would result in adapter readthrough (in the same way that I currently have to deal with read-through in Haloplex assays).
Does anyone do this for SureSelect, and if so, what are the adapter sequences that you use?
Thanks
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