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WeiWei060512 / NUMTs-detection

Detecting NUMTs from WGS
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Software version for reproducibility #4

Closed FL512 closed 1 year ago

FL512 commented 1 year ago

Dear Wei,

First of all, thank you very much for sharing a fantastic tools for us. We really appreciate it.

My colleague and I are interested in analyzing NUMTs using your established pipeline. It will be of great if we know which version of software you used in the pipeline. Typically, could you please let us know the version of perl and samtools (and blat if possible) used in NUMTs detection.sh?

Thank you in advance, Ken

https://github.com/WeiWei060512/NUMTs-detection/blob/master/scripts/NUMTs_detection.sh module load samblaster/0.1.24 module load samtools module load Sambamba/0.6.6

WeiWei060512 commented 1 year ago

Hi Ken, Thanks for reaching out. You can find the versions in our online publication.

Best, Wei

FL512 commented 1 year ago

Hi Wei,

Thank you for your response.

I found most of the version info at https://static-content.springer.com/esm/art%3A10.1038%2Fs41586-022-05288-7/MediaObjects/41586_2022_5288_MOESM2_ESM.pdf Thank you!

Do you mind if ask a few more things? Which version of the perl did you use when you established the NUMTs? Are you an Ubuntu user or a CentOS user?

Happy holidays! Ken

WeiWei060512 commented 1 year ago

I used perl 5. I ran my analysis on Genomics England Research Environment.

Wei

FL512 commented 1 year ago

Thank you again for letting me know!! Ken