Question: some problems I meet when running Bismark+DMAP
0
gravatar for hua.peng1314
5.2 years ago by
hua.peng131490
China
hua.peng131490 wrote:

Hi,

I meet some problem when running Bisnark+DMAP,The data I use is the "Test dataset 1 for DMAP"  getted from http://biochem.otago.ac.nz/research/databases-software/

The commands I used are:

bismark_genome_preparation ./

bismark -q  -n 1 -l 40 ~/projects/Methylation/BS_seq/reference1/ ../MDS_chr1_maps.fastq

bismark_methylation_extractor -s --bedGraph --counts --buffer_size 10G --cytosine_report --genome_folder ~/projects/Methylation/BS_seq/reference1/ MDS_chr1_maps.fastq_bismark.sam

diffmeth -e 40,220 -g ~/projects/Methylation/BS_seq/reference1/Homo_sapiens.GRCh37.75.dna.chromosome. -R MDS_chr1_maps.fastq_bismark.sam |awk -f ~/software/meth_progs_dist/src/getcpgpcmeth.awk >diffmeth.single.MDS.list

 

So I get two files ——the "MDS_chr1_maps.fastq_bismark.CpG_report.txt" and the "diffmeth.single.MDS.list",In the former I get these information:

1       10469   +       0       0       CG      CGC
1       10470   -       0       0       CG      CGA
1       10471   +       0       0       CG      CGG
1       10472   -       0       0       CG      CGC
1       10484   +       0       0       CG      CGG
1       10485   -       0       0       CG      CGG
1       10489   +       0       0       CG      CGC
1       10490   -       0       0       CG      CGG
1       10493   +       0       0       CG      CGC
1       10494   -       0       0       CG      CGG
1       10497   +       43      8       CG      CGG
1       10498   -       0       0       CG      CGG
1       10525   +       47      5       CG      CGC
1       10526   -       58      11      CG      CGG
1       10542   +       48      4       CG      CGA
1       10543   -       63      7       CG      CGG
1       10563   +       40      12      CG      CGC
1       10564   -       64      6       CG      CGT
1       10571   +       46      5       CG      CGC
1       10572   -       64      5       CG      CGG
1       10577   +       0       0       CG      CGC
1       10578   -       44      25      CG      CGA
1       10579   +       0       0       CG      CGG
1       10580   -       39      30      CG      CGC
1       10589   +       0       0       CG      CGG
1       10590   -       63      5       CG      CGG

and the latter:

1       10497   84.31
1       10525   86.78
1       10542   90.98
1       10563   85.25
1       10571   91.67
1       10577   63.77
1       10579   56.52
1       10589   92.65
1       10609   -
1       10617   -
1       10620   -
1       10631   -
1       10633   -
1       10636   -
1       10638   -
1       15720   -
1       15749   -
1       15769   -
1       15789   -
1       15834   -
1       15849   94.74
1       15865   94.74
1       15882   100.00
1       15912   94.74
1       17562   100.00

I don't know how to explain the differences between them such as 10577.Have I done anything wrong or it's a real bug in the software?

Moreover,the latter I think just show me the cytosine on the + strand.if right how could I get the information about the - strand.If not how could I get the information about the strand directly? I see the introduction of the options and the but couldn't get any help.

Thanks for your help

 

bismark dmap rrbs • 1.6k views
ADD COMMENTlink modified 5.2 years ago • written 5.2 years ago by hua.peng131490

You're piping things through an awk script before writing that file. What's in the awk script? Perhaps that's causing weird results (and anyway, it's hard to know what the 3rd column even means without more information).

ADD REPLYlink written 5.2 years ago by Devon Ryan90k
0
gravatar for hua.peng1314
5.2 years ago by
hua.peng131490
China
hua.peng131490 wrote:

I find the answer when I read the paper again and use the R package MethylKit. The DMAP result is depend on the both strand and the bismark depend on  just one strand.For example,the 

1       10577   +       0       0       CG      CGC and the 
1       10577   63.77. They seem different.But the 
1       10578   -       44      25      CG      CGA agrees with the 
1       10577   63.77

And this is also the answer for my second question.

ADD COMMENTlink written 5.2 years ago by hua.peng131490
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