Dong-Ha Oh

Q on coverage, multi-genome alignment, and maf2synteny

4

Hi, thanks for this fast and easy-to-run aligner :) I have two questions. 1. How the "coverage" in the report was calculated? I had a coverage value 0.95 from a...

Hi, thanks again for providing this amazing toolkit. The `fisher` command appears useful for checking the significance of overlap very quickly. But I wonder whether there is a bit more...

Information content of a custom GO annotation.

1

Hello, Thanks for developing and maintaining this amazing resource. There is [an instruction](https://github.com/tanghaibao/goatools/blob/main/notebooks/dcnt_and_tinfo.ipynb) to obtain information content for each GO term in human, mouse, and fly GOA. Could you also...

Hello, I guess the `mafStats` bundled in the Cactus installation (2.3.0) is from mafTools. :) If so, I have a few questions on how to read the results: 1. Is...

Alignment of a large genome in 2bit

1

Hello again, Bogdan and Michael, So far, `make_lastz_chains` has been working great, and the largest successfully aligned was the wheat genome (14.6 Gb). This time, I was asked to see...

Stalled at the doChainRun step

6

Hi, Bogdan and Michael @kirilenkobm @MichaelHiller, This was originally a comment on issue #9. Then, I realize it's a separate issue. When I tried human vs. Chimpanzee and human vs....

chainCleaner failure with chromosomes >1Gb (2^30)

7

Hello again, I was trying to align the corroboree frog and _X. tropicalis_ genomes. The corroboree frog genome ([GCF_028390025.1](https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_028390025.1/)) is not prohibitingly large, but it includes a chromosome larger than...

A minor discrepancy between v1.0.0 and v2.0.8 at 'fill_chain' step

4

Hi again, Recently, we have been testing `make_lastz_chains` v2.0.8 (MLC v2) to run on our SGE grid. After adding some `clusterOptions` directives to the `Nextflow` template (`execute_joblist.nf`), the MLC v2...

Using an alternative scoring matrix in make_lastz_chains v.2.0.8

2

We have been adding `BLASTZ_Q` parameter when running `make_lastz_chains` v1.0.0 (MLC v1) to use an alternative scoring matrix (HoxD55 instead of the default HoxD70) for increased sensitivity when aligning more...

Options for higher protein-to-genome alignment sensitivity

2

Dear Osamu, @ogotoh Hello again! Continuing from issues [#78](https://github.com/ogotoh/spaln/issues/78) and [#80](https://github.com/ogotoh/spaln/issues/80), we have been testing `spaln` (v.3.0.6d) to generate protein-to-genome alignments that can provide evidence for our genome annotation pipeline....