Application to Amplicon-Seq Libraries

[Rinyaveion]

Dear Tobias, I'm interested in applying SLAM-seq to investigate synthesized reporter libraries to uncover functional variants (usually SNPs) that change mRNA kinetics, in a massively parallel reporter assay. These are short (~120bp) portions of 3'UTRs, and the library has both the SNP and WT versions. Will the SLAM-DUNK pipeline work without a .bed file when aligning to a custom reference? Should I have checked NGM documentation before coming here?

Best, Anthony Fischer

[t-neumann]

Hi - it should work if you only run the map + filter steps. Alternatively, what I do is typically supplying bed files that cover all the different custom references from start to end, then you can run the full thing out of the box.