Work with mm39 genome

[FerriolCalvet]

Since there is a new version of the mice genome and this is part of bgdata and bgsignature, it would be great to add it to the list of available genomes from OncodriveCLUSTL.

this is where the options are listed:
https://bitbucket.org/bbglab/oncodriveclustl/src/2b3842ef45fef12f35b3615a0636ef62910f6350/oncodriveclustl/main.py?at=master#lines-47

And this is where the information from the genome is used:
https://bitbucket.org/bbglab/oncodriveclustl/src/2b3842ef45fef12f35b3615a0636ef62910f6350/oncodriveclustl/utils/run.py?at=master#lines-200

since it is done through bgreference as long as we make sure that the latest version of bgreference is installed with the installation requirements of oncodriveclustl I guess it should be fine!

(happy to provide test data from deepCSA)

[FerriolCalvet]

Miguel added mm39 to the list of available genomes, but this will only be reflected in if the bgreference version installed is the latest one.
When making this modification the requirements of the installation of oncodriveclustl should request bgreference v0.7 at least
https://bitbucket.org/bgframework/bgreference/commits/603424267d019a67b2415c8fe4e9904d1056b6a7

[XiaoYan000]

Hi, I am wondering if I can use the mm38 as reference, but I don't know how to prepare the file. Can you give me some guidence? Thank you very much

[FerriolCalvet]

Hi,
mm38 is not a commonly used name for mouse genomes.
If you want to use GRCm38 this is the same as mm10 which is already available in oncodriveclustl.
See: reference for mm10 genome name
I hope this helps, let me know otherwise.

[XiaoYan000]

Hi. Thank you very much for your reply. I have set -g mm10; however, it stucked. So I execute the bgdata :

bgdata get datasets/genomereference/mm10
2024-10-05 00:17:16 bgdata.manager INFO -- Tag "master" for "datasets/genomereference/mm10" resolved as 20180109
2024-10-05 00:17:16 bgdata.manager INFO -- Package "datasets/genomereference/mm10-20180109" not found in local repo
2024-10-05 00:17:17 bgdata.repository INFO -- Downloading datasets/genomereference/mm10-20180109
100% 564.2 MiB 301.9 KiB/s 0:00:00 ETA
2024-10-05 00:49:12 bgdata.package INFO -- Extracting package.tar.xz
2024-10-05 00:50:21 bgdata.repository INFO -- Package datasets/genomereference/mm10-20180109 ready
2024-10-05 00:50:21 bgdata INFO -- Dataset downloaded
/home/xiaoxinyi/.bgdata/datasets/genomereference/mm10-20180109
It seems that the file download successfully.

However, when I run oncodriveClustl, Error showed 'Sequence 'GL456210.1' not found in genome build 'mm10''. (I have already filter the chromosome:
chromosomes = set(map(str, list(range(1, 19)) + ['X', 'Y']))
gencode['CHROMOSOME_FILTER'] = gencode.apply(lambda x: 'PASS' if x['CHROMOSOME'] in chromosomes else 'FAIL', axis=1)
gencode = gencode.loc[gencode['CHROMOSOME_FILTER'] == 'PASS'].copy()
gencode.drop(['CHROMOSOME_FILTER'], axis=1)

Can you give me some advice for this bug?
Thanks a lot!

[FerriolCalvet]

Hi
I am not among the developers of the tool so I can't help a lot with this, I find it weird that if you have filtered the input this sequence raises an error so I would make sure again that this is not there, but apart from this I am afraid I can't help much.
Can you send the details on how you run oncodriveclustl after filtering these variants?

Ferriol