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Hello,
We received the raw reads of our ddRAD library from a sequencing facility, and after demultiplexing, I noticed that there is a 10-fold difference in raw read counts among samples.
We used 12 barcodes combined with 4 indexes to have 48 samples in the same sequencing run. The interesting thing is that the read numbers are always higher for the same barcodes across the 4 indeces/sublibraries. Has anyone else come across this? Is this because something we did during the library prep, e.g. PCR? Or more likely during sequencing? We are planning to prepare 4 more libraries for the same project so it would be great to fix it if possible.
We received the raw reads of our ddRAD library from a sequencing facility, and after demultiplexing, I noticed that there is a 10-fold difference in raw read counts among samples.
We used 12 barcodes combined with 4 indexes to have 48 samples in the same sequencing run. The interesting thing is that the read numbers are always higher for the same barcodes across the 4 indeces/sublibraries. Has anyone else come across this? Is this because something we did during the library prep, e.g. PCR? Or more likely during sequencing? We are planning to prepare 4 more libraries for the same project so it would be great to fix it if possible.