Hi
I have directional paired-end library for BS-seq and use bismark to analyze the data. The program runs fine. However, I notice that the read orientation is not correct. The paired reads should have opposite orientation, but bismark output shows same orientation for a pair, either on the + strand or on the - strand. I think it won't affect methylation estimation, but the visualization is not correct. Does anyone have idea how to fix it?
Here is two pairs of reads:
ID1 2/1 67 chr10 127850053 ...
ID1 2/2 131 chr10 127850058 ...
ID2 2/1 115 chr1 177168854 ...
ID2 2/2 179 chr1 177168819 ...
Thanks
I have directional paired-end library for BS-seq and use bismark to analyze the data. The program runs fine. However, I notice that the read orientation is not correct. The paired reads should have opposite orientation, but bismark output shows same orientation for a pair, either on the + strand or on the - strand. I think it won't affect methylation estimation, but the visualization is not correct. Does anyone have idea how to fix it?
Here is two pairs of reads:
ID1 2/1 67 chr10 127850053 ...
ID1 2/2 131 chr10 127850058 ...
ID2 2/1 115 chr1 177168854 ...
ID2 2/2 179 chr1 177168819 ...
Thanks
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