Dear all,
I have done a bismark alignment of high coverage bisulfite Illumina 100bp PE reads (maybe 50-60x) to a plant genome. The biologists I work with are slightly unimpressed that Cs in the chloroplast are predicted to be methylated, since they should apparently remain unmethylated.
This might be due to
1) incomplete bisulfite treatment
2) mismapped genomic DNA reads mapped to the chloroplast (for example a mapping quality problem)
3) contamination of genomic DNA by the many chloroplasts present in the leaf material used.
4) further ideas?
Which of these do you think might be more probable ?
Regards,
Colin
I have done a bismark alignment of high coverage bisulfite Illumina 100bp PE reads (maybe 50-60x) to a plant genome. The biologists I work with are slightly unimpressed that Cs in the chloroplast are predicted to be methylated, since they should apparently remain unmethylated.
This might be due to
1) incomplete bisulfite treatment
2) mismapped genomic DNA reads mapped to the chloroplast (for example a mapping quality problem)
3) contamination of genomic DNA by the many chloroplasts present in the leaf material used.
4) further ideas?
Which of these do you think might be more probable ?
Regards,
Colin
Comment