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shendurelab / MPRAflow

A portable, flexible, parallelized tool for complete processing of massively parallel reporter assay data
Apache License 2.0
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Single-end sequences to associate with the barcodes #83

Open Will19902225 opened 6 months ago

Will19902225 commented 6 months ago

Hi,

We got some issues with the pair-end sequencing Miseq. Sequences of the read 1 of enhancers were in good quality, while read2s contained many Ns. We wonder if we can use single-end sequences to associate with the barcodes.

Many thanks, Jason

makirc commented 6 months ago

In principle yes. Depends a little on your exact design, but if you have all the sequence variation covered that is required for an ambiguous identification of your target sequence in your forward read, then you can still associate. We typically do PE to cover long targets/inserts where we need the second half of the sequence to unambiguously decide between multiple sequence variants, to identify an early start of adapter sequences and/or to reduce errors in consensus calling between the two read ends.