I am working with samples of heart rejection patients. I used ONT to sequence two samples one with a slight rejection and the other with no rejection.
After that i used Guppy to generate .bam files and made .bed files from the bam using Modbam2bed. I map each CpG using the start oder end index to the Pos on the reference Atlas to map each CpG to a specific Illumina ID. And after that i use the Deconvole script.
I currently am just not seeing any left.atrium cells or Adipocytes in the samples. I just see Neutrophiles, Erythrocyte_progenitors and Monocytes_EPIC. The only difference between the samples is between the amount of Neutrophiles. So now i am wondering is there a Error in my approach of mapping or my basic Pipeline ? Am i forgetting any steps ? Cause the deconvolution results do not match what i would accept to see.
Maybe someone has experience with using ONT Data for this Algorithm and can help me out.
Hello Everyone!
I am working with samples of heart rejection patients. I used ONT to sequence two samples one with a slight rejection and the other with no rejection. After that i used Guppy to generate .bam files and made .bed files from the bam using Modbam2bed. I map each CpG using the start oder end index to the Pos on the reference Atlas to map each CpG to a specific Illumina ID. And after that i use the Deconvole script.
I currently am just not seeing any left.atrium cells or Adipocytes in the samples. I just see Neutrophiles, Erythrocyte_progenitors and Monocytes_EPIC. The only difference between the samples is between the amount of Neutrophiles. So now i am wondering is there a Error in my approach of mapping or my basic Pipeline ? Am i forgetting any steps ? Cause the deconvolution results do not match what i would accept to see.
Maybe someone has experience with using ONT Data for this Algorithm and can help me out.
Thanks in advance! kind regards, Azlan