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yanboANU / Kmer2SNP

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Error in findGSE #7

Closed stefanerb89 closed 3 years ago

stefanerb89 commented 4 years ago

Hello,

my command is "sh $path_to_kmer2snp 31 30 1.fastq,2.fastq,3.fastq

I get the following error even when I change the parameters k and coverage:

Error in findGSE(histo = args[1], sizek = args[2], outdir = args[3], exp_hom = strtoi(args[4])) : 
  No k-mer freq peak was found with the cutoff given by -exp_hom.
                  You may need to increase the cutoff!

What I am doing wrong?

yanboANU commented 4 years ago

You may give the wrong coverage. findGSE estimates heterozygous peak and homozygous peak according to the coverage you given.

From: stefanerb89 notifications@github.com Sent: Thursday, September 24, 2020 8:29 PM To: yanboANU/Kmer2SNP Kmer2SNP@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: [yanboANU/Kmer2SNP] Error in findGSE (#7)

Hello,

my command is "sh $path_to_kmer2snp 31 30 1.fastq,2.fastq,3.fastq

I get the following error even when I change the parameters k and coverage:

Error in findGSE(histo = args[1], sizek = args[2], outdir = args[3], exp_hom = strtoi(args[4])) : No k-mer freq peak was found with the cutoff given by -exp_hom. You may need to increase the cutoff!

What I am doing wrong?

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stefanerb89 commented 4 years ago

Thank you for your comment! It is exome capture data. Maybe it's because only exons have high coverage (30x). Average coverage is only 1.4 ?