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-   -   Methylation: Igv and bismark question (http://seqanswers.com/forums/showthread.php?t=84614)

iz8wok 09-13-2018 11:16 PM

Methylation: Igv and bismark question
 
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Hi i have a question, i working for first time with bismark, after alignment i watched the results on IGV. Why each column methylated contains cytosine and tymine? spontaneous deamination? (Watch image attached)

I have file paired-end and i use this command line:

bismark --multicore 6 --non_directional /genomes/ -1 file_R1.fq.gz -2 file_R2.fq.gz

why the file .bam seems a Single-end alignment??
thank you
Giuseppe


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