This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Quake Coverage Cutoff output

Hello I am trying to run the Coverage cutoff module of Quake Error Corrector. i get output files called cutoff.txt and kmers.hist

My Cutoff.txt output is as follow:

1 zp.copy: 0.8268095 p.e: -50570.72 shape.e: 253.7109 u.v: 73.32117 var.v: 507.014 -18066.49 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

Can anyone help me understand this file? I could not find anything on the manual and my result seems ambiguous. Is my coverage cutoff value 1?

quake cov_model.py
• 1,811 views • link
written by Seigfried Seigfried

At the bottom of your cov_cutoff_"kmer_size" file you you should see 'Cutoff: #'. That number should be your cutoff value given the value of the kmer you used.

• 0 views • link
written by st.ph.n st.ph.n

1 answer

the current Cov_model lists the CUtoff at the end on the command line.

In the file produced the cutoff is the "1" the first number in the file.

• 0 views • link
written by Seigfried Seigfried

Log in to answer this question.

More posts like this
  • Quake Error Corrector
    written by Seigfried Seigfried
    Hello I have been trying to run Quake Error Corrector on my Illumina reads before assembly. I am following the manual at [http://www.cbcb.umd.edu/software/quake/manual.html][1]. I have …