Question: fastqc file showing bad result for tile kmer
0
gravatar for analytical
2.6 years ago by
analytical0
india
analytical0 wrote:

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

fastqc fail kmer tile wgs • 820 views
ADD COMMENTlink modified 2.6 years ago by YaGalbi1.5k • written 2.6 years ago by analytical0
0
gravatar for YaGalbi
2.6 years ago by
YaGalbi1.5k
Biocomputing, MRC Harwell Institute, Oxford, UK
YaGalbi1.5k wrote:

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

ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by YaGalbi1.5k

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?

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by analytical0
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