JIANHONG OU

Hi Stephen, Thank you for trying ATACseqQC. Indeed this is a big issue of ATACseqQC. This is on my schedule. Now the function readBamFile will read the whole bam file...

Hi Stephen, It is hard for me to provide an ETA. But I will do it as soon as possible. Jianhong. On Sat, May 5, 2018 at 9:34 AM, Stephen...

Hi Stephen, I tried to fix the memory issue of ATACseqQC. Please have a try with the newest development version of ATACseqQC to see the changes. Jianhong.

Hi hkoohy, try to run splitBam without providing the conservation argument to see if it still kill the memory. I will try to figure out this issue.

Did you tried to set bigFile to TRUE and readBamFile like this gal

I got it. I did not put it as an argument for splitBam. Try to change objs

you are very welcome. Memory cost is a big issue for this package. I am trying to fix it. However, I don't have a timeline yet. On Tue, Dec 11,...

The counts number is calculated by the 5' ends or fragment center depend on your setting. Default is the 5' ends. And normalized by the factor of library size/coverage size.

Sorry for the late reply. Do you mind also share the shape of fragment size plot?

Hi Hiroko, Thank you for reporting this issue. I am writing the new export method to replace the export method in rtracklayer. The issue should be fixed in next building....