methods section

Important

This is draft method for Subproject “A”

Nutrient exposure experiment - P verrocosa genome

Warning

I have some concern about quality of genome

DNA Methylation Analysis

Deduplicated Alignment files (BAMs) were downloaded from Becker

Methylation levels were extracted

${bismark_dir}/bismark_methylation_extractor \
--bedGraph --counts --scaffolds \
--multicore 28 \
--counts \
--comprehensive \
--merge_non_CpG \
--buffer_size 75% \
*deduplicated.bam

This was followed by coverage file generation

find *deduplicated.bismark.cov.gz \
| xargs basename -s _R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz \
| xargs -I{} ${bismark_dir}/coverage2cytosine \
--genome_folder ${genome_folder} \
-o {} \
--merge_CpG \
--zero_based \
{}_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz

and files generated for downstream analysis.