Question: Converting Bisulfite-seq BAM files to fastq
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gravatar for divyswar01
11 months ago by
divyswar010
divyswar010 wrote:

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.

ADD COMMENTlink modified 9 months ago by Biostar ♦♦ 20 • written 11 months ago by divyswar010

Hi, is it an old sequencing ? Do you know the technology used (maybe the aligner consider an older phred score ? ) ? I'm a bit surprise because the BAM files is generated in a way to conserved the original quality of sequencing bases so i couldn't imagine an original fastq with better bases qualities.

ADD REPLYlink written 9 months ago by Titus860
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