Question

Minimal input data format for bsseq

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Martin Aryee ▴ 20

@martin-aryee-5585

Last seen 7.5 years ago

Boston, MA, USA

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 Sequencing Alignment bsseq • 1.6k views

ADD COMMENT • link updated 11.9 years ago by Kasper Daniel Hansen ★ 6.5k • written 11.9 years ago by Martin Aryee ▴ 20

score 0 · Answer 1 · 2012-12-21

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}}