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
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