TCGA has some DNA Methylation files here https://portal.gdc.cancer.gov/legacy-archive/search/f. But they only have BAM files here. I need fastq files for these BAM files. I have contacted GDC and they said they only have BAMs available. Since fastqs in bisulfite context are aligned with Bisulfite-aware aligner, I don't think converting BAM to fastq is straightforward. I tried using samtools bam2fq function and it produces fastq files containing reads with very low base quality and excessive amount of repeats. When I aligned these converted fastqs I got almost 0 alignment rate.
I am wondering if there is a way to convert bisulfite sequencing BAMs back to fastqs. It would be more convenient if TCGA had fastqs available but since that is not an option I am not sure how to regenerate the fastqs.