mgatk
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caleblareau
mgatk: mitochondrial genome analysis toolkit
Hello, I've been following the wiki to try to run mgatk tenx (v0.6.1) on 10x scRNA data using the following command: ``` mgatk tenx -bt CB -g mm10 --snake-stdout -c...
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...
**Describe the bug** Hi, I've been trying to run mgatk on the test files provided here but the output files are not quite right on the `logs` folder. This is...
Found bam file: /home/i439h/projects/heroes-aya-pools/AG_Thongjuea/Result/10x_multiomics/CellRanger_ARC/1016715_pool3_hg38/outs/gex_possorted_bam.bam for genotyping. Wed Mar 20 12:38:37 CET 2024: Found file of barcodes to be parsed: /home/i439h/projects/heroes-aya-pools/AG_Thongjuea/Code/bulkWGS/Sadeghi/mgatk/barcodes.tsv Wed Mar 20 12:38:39 CET 2024: User specified mitochondrial genome...
I am following the Wiki to run: (see the screenshot attached) All my bam and tsv files are generated correctly but when I am trying run the .sh file attached,...
Hopefully resolves #70. It does for me on the test files at least. Very minor edits: - Adds matplotlib to the dependencies - Rplaces deprectated `np.float` with `float`
Would you consider making a conda package for mgatk? In the process of trying to resolve #70, I've been going through the code, and have a couple of observations. 1....
Hi team, Thanks for sharing this very useful tool. I ran mgatk tenx using my own scATACseq data. `mgatk tenx -i possorted_bam.bam -n mytest -o mytest_mgatk -c 8 -bt CB...
`np.float` was deprecated in NumPy v1.20 and removed in v1.24. Using mgatk with the latest NumPy release causes an error, resulting in the absence of output files such as `*.variant_stats.tsv.gz`...
**Describe the bug** Hi again! Continue with #85 where I'm running a atac-seq dataset with unequal R1 and R2 read lengths as I trimmed the low-quality area of R1 after...
