Alex Nesta

Hi, I see this issue is still open. I am having an issue with group_by on a large granges object with 320 thousand groups and about 2.5 million rows total....

I think you will see NAs if there are not enough reads at the splice junction to accurately quantify the splicing event. Can you check your bam in IGV to...

Just repeated with a fresh install of everything and using sample data. Same error. Sorry it's a lot to read through: ```(base) [nestaa@sumner030 ORQAS2]$ conda create -n orqas2-env python=3.5 Collecting...

UPDATE: Tried with a fresh ubuntu VM instead of using my university cluster. Same error. Getting closer... Definitely an issue with the riboprof step of ribomap: I believe I am...

I wrote a hack to get it working for the most part. The issue seems to be that the line headers of the quant.sf are read into riboprof and cause...

I believe the issue is the output file column names. Not sure if it was a software version mismatch? Hopefully that narrows things down. A docker/singularity container might help eliminate...

I ended up manually creating the discordants and splitters before running lumpy express. It seemed to bypass the issue.

Sorry Ryan, I went to share it and realized that previous comment was incorrect. I have since edited the comment to show that there is a way to bypass the...

same issue here also. Anaconda 4.2.0 Python 2.7.14 venv hexdump in /usr/bin/hexdump did conda install numpy and pysam... and both were already installed `./lumpyexpress: line 15: -n: command not found`...

The only way I was able to get lumpy to run at all and avoid this error was the following: use bamaddrg and make sure you have readgroups added to...