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zhou-lab / biscuit

BISulfite-seq CUI Toolkit
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meaning of vcf2bed output #20

Open vanhzh opened 7 years ago

vanhzh commented 7 years ago

Hi Wanding Zhou,

Thank you very much for the software! I have a few maybe very stupid questions. I have never worked with NOME-seq or BS-seq before.

My command is: biscuit vcf2bed -c -t gch sample.vcf | head I got: chr1 87271 87272 0.000 3 G GCH chr1 564682 564683 0.650 20 C GCH

Would you please elaborate a little on what each column from the 4th column means?

In addition, I tried to detect ndr

My command is: biscuit vcf2bed -t gch -c sample.vcf | biscuit ndr -c -b - | head

I got: chr1 87272 3 0 chr1 564683 20 13 chr15 28703185 28704388 chr15 28704545 28704619

Would you please explain a bit on the meaning of each column in output? Would you also explain a bit on the difference between chr1 and chr15?

Thank you very much for your help in advance!

Best,

Zhehua

zwdzwd commented 7 years ago

Hi, the 4rd column is similar to beta value which is M/(M+U). M is the count of cytosine retention and U is the count of conversion. In the case of nome-seq, you could view it as the percentage of nucleosome accessivity (higher the value, more accessible). The ndr function is still under development. We are in the middle of fleshing out the documentation.

Thanks,

vanhzh commented 7 years ago

Hi Wanding,

Thanks very much for your helps. Maybe I am too greedy but I wonder if it is possible to add an extra column with actual number of Ms, in addition to columns of M/(M+U) and (M+U)

Thanks again and have a good day!

Best,

Zhenhua From: Wanding Zhou - Bioinformatics [mailto:notifications@github.com] Sent: Thursday, 8 June, 2017 2:14 AM To: zwdzwd/biscuit Cc: Zhenhua HU; Author Subject: Re: [zwdzwd/biscuit] meaning of vcf2bed output (#20)

Hi, the 4rd column is similar to beta value which is M/(M+U). M is the count of cytosine retention and U is the count of conversion. In the case of nome-seq, you could view it as the percentage of nucleosome accessivity (higher the value, more accessible). The ndr function is still under development. We are in the middle of fleshing out the documentation.

Thanks,

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