Open ttab963 opened 1 year ago
Hm strange... it's erroring out at not finding a 'depth' file per barcode; can you see if this command works?
mgatk bcall -i barcode/test_barcode.bam -n bc1_tenx -o tenx_test -bt CB -b barcode/test_barcodes.txt -z
Thank you for your reply. Unfortunately it shows same error.
But interesting point is if i run again with -z option to the same directory, it runs well! I think some problem in snakemake cause the problem to find file or something. I test this on snakemake version 7.7.0 & 7.8.5.
And plus, can I use this tools to 10x single-end (3' or 5') scRNA seq data? In this case filtering method that used in this tool(strand bias) have to be changed, but i just not sure I can or not.
hello, I met the same error as u mentioned, did u figure out what cause the problem? how to solve the problem? and what do u mean "run again with -z option to the same directory,"?
Hi, team. I tried to use MAESTER(https://github.com/petervangalen/MAESTER-2021), and maegatk first. But in my own data or test data cannot be processed, so i tried to mgatk test file. Then i figured out this problem is also happed in mgatk.
I ran this command,
Error comes out after final_sparse_matrices part.
and
These are the list of output files.
I really appreciate your kindness. Thanks.