Yilei Fu
Yilei Fu
Could you please attach one read from your bam file? I am suspecting there are some bugs with the methylation signal reading. Thanks! Get Outlook for iOS ________________________________ From: Wshengquan...
I see. The read you are showing here only has 6mA calls, but MethPhaser can only phase with 5mC calls.
MM:Z:A+a? is for 6mA calls. C+m? is for 5mC.
I see, yes indeed this is a bug of MethPhaser. I would suspect that there are some reads that only have 6mA calls but do not have 5mC calls. I...
I've made the changes, could you please check the MethPhaser version of (https://github.com/treangenlab/methphaser/tree/Fu-Yilei-patch-1)? Or if you could provide an example BAM file I can do the test.
yeah you need to clone the version in the branch I provided
sorry forgot to change one spot in the code, now should be fine :)
Sorry about the back and forth. Was this the program from this patch? https://github.com/treangenlab/methphaser/tree/Fu-Yilei-patch-1 Based on the line number of the bug, it seems like you are using the main...
you could limit your vcf, gtf and bam to the first 3 phaseblock on chr1. I think those could be sufficient. Thanks.
Hey no worries! For gtf file, keep only first 3 lines. For bam file, use samtools with samtools view function with specifying region chr1:0-x (x = the phaseblock end of...