Jennifer Polinski

My transcript headers, from Trinity assembly, are in the format ">TRINITY_DN4342|c0_g1_i1", where the g indicates the gene and i indicated isoform. In my output tsv file, all the characters after...

test_driver.py failure - "CUDA header does not match"

1

I am getting the following error when I run "test_driver.py": ``` `python3 test_driver.py /usr/local/lib64/python3.6/site-packages/pycuda-2021.1-py3.6-linux-x86_64.egg/pycuda/driver.py:71: UserWarning: Failed to import the CUDA driver interface, with an error message indicating that the version...

Can I resume pipeline based on where left off?

1

Due to memory issues, my pipeline failed during samtools sorting of the files. I was able to sort the files outside of the pipeline and would like to have it...

Karyotype "Error: some genes in blocks can't be found, please rerun after making sure that bed file agree with simple file."

6

I can trying to create a macrosynteny figure with 3 genomes, but keep getting the error that the genes in the second simple file cannot be found in the bed...

Test run failed at map_genome: "[gzclose] buffer error"

3

I just installed NextPolish but am getting errors when I try to run the test data that results in "map_genome failed". The final line in the nextPolinski.sh.e files is "[gzclose]...

Rooted species tree branch length meaning

2

How are the branch lengths calculated/what do they represent in the rooted? Rate of gain/loss, divergence time, etc.? This question was posed by a reviewer regarding a figure that includes...