Hi,
I'm having a problem with one of my sample!

I analysed it with fastqc and it shown the Quality score between 30 and 40 (I attached the pic), but when i looked the kmer (attacehd pics) it looked awful! I don't understand what it is and why it shows a good quality if my sequences are not good at all!! The analysis is terribile: I'm not able to identify SNP/indel and the coverage is low!! Do you know what it's going on with this sample?? And do you know if there is a way to clean or to restore it??
Thanks!!
M
I'm having a problem with one of my sample!


I analysed it with fastqc and it shown the Quality score between 30 and 40 (I attached the pic), but when i looked the kmer (attacehd pics) it looked awful! I don't understand what it is and why it shows a good quality if my sequences are not good at all!! The analysis is terribile: I'm not able to identify SNP/indel and the coverage is low!! Do you know what it's going on with this sample?? And do you know if there is a way to clean or to restore it??
Thanks!!
M
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