Hi,
I am trying to understand which read to consider file for methylation value calculation from the bam file generated by BISCUIT? Also how to figure out which is "C strand" and "G strand" from the generated bam? For example, in the following biscuit tview image, there are 14 non duplicated reads (all has mapq=60) for the highlighted CpG.
However, the generated bedgraph file is saying that the total depth is 10.
Will you please explain what I am missing here? I have also attached the corresponding sample sam file (for some reason can not attach the bam file) if you want to reproduce it. Thanks
Hi, I am trying to understand which read to consider file for methylation value calculation from the bam file generated by BISCUIT? Also how to figure out which is "C strand" and "G strand" from the generated bam? For example, in the following biscuit tview image, there are 14 non duplicated reads (all has mapq=60) for the highlighted CpG.
However, the generated bedgraph file is saying that the total depth is 10.
Will you please explain what I am missing here? I have also attached the corresponding sample sam file (for some reason can not attach the bam file) if you want to reproduce it. Thanks
corres_pos_cgr1-1222701_nodup.txt