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fastqc file showing bad result for tile kmer
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2.8 years ago
analytical • 0
india

Hi all

I have WGS for snps analysis the quality of bases and GC content for all my 3 samples are good No adapter sequence fail reported in fastqc library was prepared with NEB adapters But still i am getting fail and warning with Kmer and tile

How should i tackle this or is it fine to ignore it if it is WGS sequence for snps data analysis

Sample1_1 tile and kmer

https://ibb.co/nqmrBb

https://ibb.co/gsfjWb

Sample1_2 tile and kmer

https://ibb.co/jMhsHG

https://ibb.co/cscRcG

Sample2_1 kmer

https://ibb.co/iPqF4w

Sample2_2 kmer

https://ibb.co/jykyPw

Sample3_1 tile

https://ibb.co/nBm2HG

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2.1 years ago
YaGalbi ♦ 1.4k
Biocomputing, MRC Harwell Institute, Ox…

What is the result in the over-represented sequences section? - I'm guessing you'll see some overrepresented sequences that once removed will fix the kmer problem

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No Overrepresented sequence were found in my data all the data. Also if tiles has this issues will it not create problem while calling SNPS or Indel?

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