W16: Library Prep for NGS- Day 1

This workshop will cover the basis of Next-Gen Sequencing Library Preparation for Illumina Sequencers. Different Library Preparation Techniques (DNA-seq, ChIP-seq, RNA-seq, Methyl-seq) are explained the first and second day in class. The third day, Quality Control steps of the starting input material and final libraries are performed in the Lab (TapeStation). Purification from Primer Dimers (using AMPure beads) and Library Submission is also performed on the same day.

[gazeloykumozdemir]

Thank you for the video ! Please keep posting.

[jkim]

A first few sequence have weired GC percent due to the enzymatic fragmentation 42:00
Index info 46:00
Final library shape - Y shape adapter 59:15
adapter/primer dimers 1:14:00
P5 index2 5' R1, p7 index1 3' R2 1:42:00
Nextera library prep needs Amplification - PCR, while Trueseq nano - No PCR 2:05:00

[samtheammyk]

1:44:01 I'm a little confused. How can you sequence read two when the adapters on both strands are oriented in the same direction. I think DNA can only be sequenced 5' to 3'. Wouldn't the bottom strand need to be flipped around in order for read 2 to be sequenced? I don't understand how read 1 and read 2 and be read in opposite directions when both DNA stands are oriented in the same direction.

[canyonbreeze]

I just can't stand the too frequent "Ahn, Ahn,