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tommyau / bamclipper

Remove primer sequence from BAM alignments by soft-clipping
MIT License
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Primer Extension Methods #5

Closed crutching closed 6 years ago

crutching commented 7 years ago

Hi there,

I'm curious about paired-end designs utilizing a single primer. Is this something that BamClipper can handle?

Thanks!

tommyau commented 7 years ago

We recently developed a variant of BAMClipper to handle single primer extension dataset but I am not sure whether it fits your dataset. Is your dataset based on a commercially available gene panel like Qiagen Qiaseq? or ArcherDx?

crutching commented 7 years ago

Great, I'd love to try it out! Otherwise, I will be writing my own. Yes, this is based on the QIAseq method, with UMIs. I'm feeling good about adapter and UMI handling, now just trying to deal with the error rate in primer regions leading to incorrect allele frequency estimation.

marcelcaraciolo commented 7 years ago

We would also like to test it. Is it possible ?

tommyau commented 7 years ago

Please contact chau@hksh.com for further discussion. Thank you.