When performing target enrichment of large panels of genes using a PCR based method such as Fluidigm or Raindance, primers of varying lengths are used to amplify targets. I am looking for a tool to remove the known primer sequences. I know Illumina has incorporated such a tool in the miseq reporter for truseq custom amplicons, but I have not been able to find a similar tool to incorporate into the standard CASAVA (or other) pipelines. I contacted Illumina about this, but, of course, they were no help. I have also attempted to use cutadapt, but it is not working. And, since the primer sequences are of varying length, I cannot simply remove X number of bases at the beginning of the read.
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Originally posted by frozenlyse View PostIn my pipeline for MiSeq amplicon analysis I align the reads keeping the primers on, and then just ignore the primer areas in downstream analysis.--
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