Hi everyone!
I am trying to trim resulting amplicon reads from Haloplex and sequenced with MiSeq.
I've found some information : http://seqanswers.com/forums/showthr...light=haloplex. In fact, the user swNGS says that he have a well defined protocol to trim those sequences. However, I've just found a technical note from Illumina (Mutation Detection and CNV Analysis
for Illumina Sequencing data from HaloPlex Target Enrichment Panels using NextGENe Software for Clinical Research) reagrding the NextGene software, saying that there is no 5' adapter sequences and just a pair of 3' sequences.
As far as I know, the resulting amplicons from HaloPlex are constructions like:
PCR_primer-----Illumina_adaptor-----target-----Illumina_adaptor-----Barcode-----PCR_primer
Should I trim just by Illumina adaptors or PCR_primers should be removed too??
Any advice will be appreciate!
I am trying to trim resulting amplicon reads from Haloplex and sequenced with MiSeq.
I've found some information : http://seqanswers.com/forums/showthr...light=haloplex. In fact, the user swNGS says that he have a well defined protocol to trim those sequences. However, I've just found a technical note from Illumina (Mutation Detection and CNV Analysis
for Illumina Sequencing data from HaloPlex Target Enrichment Panels using NextGENe Software for Clinical Research) reagrding the NextGene software, saying that there is no 5' adapter sequences and just a pair of 3' sequences.
As far as I know, the resulting amplicons from HaloPlex are constructions like:
PCR_primer-----Illumina_adaptor-----target-----Illumina_adaptor-----Barcode-----PCR_primer
Should I trim just by Illumina adaptors or PCR_primers should be removed too??
Any advice will be appreciate!
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