Does anyone know what the exact primer sequences are for the cancer panels? I really need to know so I can remove them during the alignment step. Otherwise it causes certain indels to be missed.
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Hi there,
After logging in to the AmpliSeq Designer website, navigate to the Ion Panels page. From there you can choose to 'Download panel files" for the panel you need. The pop-up window describes the contents of all the files in the zip archive, including the *.primerDataSheet.csv file to which you are referring.
I would also recommend follow up with your local Field Bioinformatics Scientist if you have any questions about analysis of the data with which they may be able to assist.
Originally posted by RockChalkJayhawk View Post -
Thanks Torrent!Comment
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aren't the majority of the primer sequences removed in the library protocol?Comment
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Not sure. All I know is that there are several 9-15bp indels that are Sanger validated that are not getting aligned. I know BWA will not usually align reads with indels > 8bp, but Novoalign does. Basically, I'm trying to develop a "Best Practices" workflow for high coverage amplicon sequencing. Too many assumptions are invalid if we use the workflow for 30X exome.Originally posted by snetmcom View PostComment
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are you using the ampliseq analysis template? i would assume it handles this data with tmap.Comment
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