JIANHONG OU

Could you show me your sessionInfo?

please try to update ATACseqQC to 1.6.0.

Hi Wangjiawen, This is a issue in package MotIV. You can add link path in ~/.R/Makevars like this: LDFLAGS: -L/path/to/you/local/lib see details at https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Using-Makevars or google: Makevars. Let me know...

how do you set /path/to/you/local/lib?

try to add one more line in your ~/.R/Makevars: CFLAGS=-I/path/to/your/gsl/include

Sorry for the late reply. I think this is correct and same as it shown in the documentation.

Did you checked the sequence length of gal1, genome and phastCons100way.UCSC.hg38? Are they identical to each others?

Thank you for trying ATACseqQC. Yes, you are correct. It should be fine with the bamFile object. But for BamFileList is still not supported yet. Currently, I am still working...

Thank you for your suggestion. fragSizeDist will accept index in next build. You can git clone it now. Yes yieldSize should help to reduce the memory cost. However, it is...

You may want to check the documentation of ?readBamFile about the flag section.