twist exome panel analysis

Question

[1769mkc]

I'm looking through various workflows for running twist exome analysis.

One of the query I have is do i need to run deduplication step before going into downstream? As After running removing duplicates in few samples I do observe quite a read reduction, as an example in the raw data I had around 20M reads after removing duplicates it comes around 9M reads.

So is it advisable to run the removing duplicates step before doing the downstream analysis.

Answer 1

[GenoMax]

do i need to run deduplication step before going into downstream?

Yes. Based on their recommendation. https://www.twistbioscience.com/blog/science/exome-sequencing-101-part-4-data-analysis

as an example in the raw data I had around 20M reads after removing duplicates it comes around 9M reads.

Twist exome targets 33 Mb of CCDS sequences. As long as you have good coverage across the targeted regions, that should be ok.

[1769mkc]

Based on the info what i see is this

[1769mkc]

"For exome sequencing experiments, the coverage standard for confidence in an experiment is 20x – that is, 20 sequenced fragments align with a nucleotide of interest. "

This is what was put in that blog.

Now the data what I see is this something of this range. Is it advisable to proceed?

[GenoMax]

With the exception of one sample looks like others have adequate coverage.