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Hello everybody!
I would like to ask for some help with files obtained with methratio script from bsmap.
I'm doing a RRBS analysis with BSMAP and MethylKit. I've seen that I have to calculate the methylation ratio from the sam files using the methratio.py script, and read them by using "pipeline" argument in read() function of methylkit. My problem comes from the new version methratio.py (I'm using the 2.90), in which there are more columns than in old versions, but I cannot find the column corresponding to the coverage.
I've seen in this web http://zvfak.blogspot.com/2012/10/ho...ion-ratio.html, that the equate the column 6 from the old version (the one called "total_C") with the new "C_count", is this correct?
Thank you very much in advance!!
I would like to ask for some help with files obtained with methratio script from bsmap.
I'm doing a RRBS analysis with BSMAP and MethylKit. I've seen that I have to calculate the methylation ratio from the sam files using the methratio.py script, and read them by using "pipeline" argument in read() function of methylkit. My problem comes from the new version methratio.py (I'm using the 2.90), in which there are more columns than in old versions, but I cannot find the column corresponding to the coverage.
I've seen in this web http://zvfak.blogspot.com/2012/10/ho...ion-ratio.html, that the equate the column 6 from the old version (the one called "total_C") with the new "C_count", is this correct?
Thank you very much in advance!!