Anjali Chawla

Hi Brian, I am working with humans. I am trying to figure out a way to determine chrX heterozygosity using "PL" which as you guessed, is absolutely correct, is the...

Hi Brian, Thanks for the example! I am trying to address if chrX is heterozygous. I believe in that case, I should extract the second element using mapsplit? Since, PL...

Hi Brian, Thanks for the clarification. You are right. I am wondering in that case, how could I assess heterozygosity for a sample? Since GT may not tell anything about...

Thank you very much, Brian for your opinions and advice.

Hi, the above issue started happening after I tried adding chromVar matrix which also throws an error. proj FUN -> %>% -> h5ls Execution halted

Hi @rcorces, I used an uncorrupted version of my ArchR project and tried adding HOMER annotations as described in tutorial. Please see error and log file attached here. [ArchR-addDeviationsMatrix-48c01d7b518-Date-2022-10-17_Time-03-23-08.log](https://github.com/GreenleafLab/ArchR/files/9800962/ArchR-addDeviationsMatrix-48c01d7b518-Date-2022-10-17_Time-03-23-08.log) [error.log](https://github.com/GreenleafLab/ArchR/files/9800969/error.log)...

In the log file - this is the error: 2022-10-17 03:47:41 : ERROR Found in .computeDeviations for atac_A10B10 (6 of 42) LogFile = ArchRLogs/ArchR-addDeviationsMatrix-48c01d7b518-Date-2022-10-17_Time-03-23-08.log **

Hi @rcorces , yes this worked. Thanks for your time.

Hi @rcorces, I looked into my scripts and it seems like ultimately the error was resolved through re-installation of master branch. Sorry, I got this mixed up with all the...

Hi @HelenaLC you are correct. It is indeed related to the filtering issue. When I say min_cells=10 with DESeq2 - it works and min_cells=5 with edgeR also works. There is...