Question: Minimal input data format for bsseq
0
gravatar for Martin Aryee
6.6 years ago by
Martin Aryee20
Boston, MA, USA
Martin Aryee20 wrote:
Hi Kasper, I'd like to use bsseq on a partially preprocessed whole genome bisulfite sequencing dataset. I have a data table with one row per CpG and columns for: 1. chromosome 2. position 3. number of reads supporting an unmethylated CpG (U) 3. number of reads supporting a methylated CpG (M) Is it possible to turn this into an acceptable input for bsseq (perhaps with reduced functionality), or is it essential to run the BSmooth alignment suite to generate the complete set of columns typically used by bsseq? Thanks, Martin The information in this e-mail is intended only for the ...{{dropped:11}}
sequencing alignment bsseq • 763 views
ADD COMMENTlink modified 6.6 years ago by Kasper Daniel Hansen6.4k • written 6.6 years ago by Martin Aryee20
Answer: Minimal input data format for bsseq
0
gravatar for Kasper Daniel Hansen
6.6 years ago by
United States
Kasper Daniel Hansen6.4k wrote:
This is all you need. Look at the bsseq constructor. Kasper On Fri, Dec 21, 2012 at 6:40 PM, Aryee, Martin,Ph.D. <aryee.martin at="" mgh.harvard.edu=""> wrote: > Hi Kasper, > > I'd like to use bsseq on a partially preprocessed whole genome bisulfite sequencing dataset. I have a data table with one row per CpG and columns for: > > 1. chromosome > 2. position > 3. number of reads supporting an unmethylated CpG (U) > 3. number of reads supporting a methylated CpG (M) > > Is it possible to turn this into an acceptable input for bsseq (perhaps with reduced functionality), or is it essential to run the BSmooth alignment suite to generate the complete set of columns typically used by bsseq? > > Thanks, > Martin > > > > > The information in this e-mail is intended only for th...{{dropped:8}}
ADD COMMENTlink written 6.6 years ago by Kasper Daniel Hansen6.4k
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