Hi,
I meet some problem when running Bisnark+DMAP,The data I use is the [Test dataset 1 for DMAP](http://biochem.otago.ac.nz/assets/software/test_MDS_data_large.tar.gz) 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
•
written
by
hua.peng1314
1 answer
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.
•
written
by
hua.peng1314
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