My M-bias plots from urine cell free are trailing off at the end and I am just trying to work out what might be causing this.
We performed methylation sequencing of a cohort of plasma and urine samples in cancer patients, with EM-seq, applying target enrichment with the twist human methylation panel (123Mb), Illumina sequencing then alignment/trimming/methylation calling etc. with nf-core methylseq, Bismark pipeline.
The M-bias plots from the plasma sample all look pretty flat, but in all the urine samples, methylation is higher at the beginning of the read and tails off considerable about mid-way through, for the CpG methylation of
We are seeing this pattern with plasma and urine samples that were sequenced on the same lane, and seen in urine samples processed in entirely different batches and sequencing runs.
Any thoughts as to what might be causing this, if anyone else has seen similar with urine samples or suggestions to investigate further?
Urine Mbias CpG read 1:
Urine Mbias CpG read 2:
Plasma Mbias CpG read 1
Plasma Mbias CpG read 2
My M-bias plots from urine cell free are trailing off at the end and I am just trying to work out what might be causing this.
We performed methylation sequencing of a cohort of plasma and urine samples in cancer patients, with EM-seq, applying target enrichment with the twist human methylation panel (123Mb), Illumina sequencing then alignment/trimming/methylation calling etc. with nf-core methylseq, Bismark pipeline.
The M-bias plots from the plasma sample all look pretty flat, but in all the urine samples, methylation is higher at the beginning of the read and tails off considerable about mid-way through, for the CpG methylation of
We are seeing this pattern with plasma and urine samples that were sequenced on the same lane, and seen in urine samples processed in entirely different batches and sequencing runs.
Any thoughts as to what might be causing this, if anyone else has seen similar with urine samples or suggestions to investigate further?
Urine Mbias CpG read 1:
Urine Mbias CpG read 2:
Plasma Mbias CpG read 1
Plasma Mbias CpG read 2
