nanoporetech
Differential methylation scoring
Good day, I would like to perform Differential methylation scoring. Is there a way to identify the number of hypo and/or hyper differentially methylated regions in introns, exons, promoters, TSS, 5′UTRs etc of a sample?
Hello @setshabaTaukobong,
What I would do is run modkit dmr pair with --regions ${bed_file} where the bed_file contains your introns, exons, promoters, TSS, etc. You can find some instructions for how preare the data and how to run this analysis in the linked documentation. With the results in hand, I would rank them by score and then look at IGV to verify the results.
@ArtRand thank you for responding. And how would you determine hyper or hypo methylated regions? I downloaded a bed file of the specific regions and then ran the following command:
modkit dmr pair -a /mnt/lustre/groups/CBBI1617/MKP035_BreastCancer/BreastCancer-methylation/BC6_BC7-methyaled/BC6-control/cpg-pileup.bed.gz --index-a /mnt/lustre/groups/CBBI1617/MKP035_BreastCancer/BreastCancer-methylation/BC6_BC7-methyaled/BC6-control/cpg-pileup.bed.gz.tbi -b /mnt/lustre/groups/CBBI1617/MKP035_BreastCancer/BreastCancer-methylation/BC6_BC7-methyaled/BC7-methylated/cpg-pileup.bed.gz --index-b /mnt/lustre/groups/CBBI1617/MKP035_BreastCancer/BreastCancer-methylation/BC6_BC7-methyaled/BC7-methylated/cpg-pileup.bed.gz.tbi -o dmr_results.txt -r New.bed --ref /home/staukobong/lustre/GCF_000001405.40_GRCh38.p14_genomic.fna --base C --threads 8 --log-filepath dmr.log
I however get the below error:
reading reference FASTA at "/home/staukobong/lustre/GCF_000001405.40_GRCh38.p14_genomic.fna" loaded 196048 regions loading 12 regions at a time Error! no valid regions in input
Not sure if my bed file is the issue.
but the bed file looks like the attached image
