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qltanGS / multi-ancestry_smoking_TWAS

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All analysis are blank #2

Open AlexHatoum opened 1 week ago

AlexHatoum commented 1 week ago

Hello,

I was hoping to run a similar analysis to your paper. In my case, I am using MA-FOCUS. MA-FOCUS works great with it's prebuilt database (focus.db), but when I run the databases from your manuscript, I get results as a blank file. I have my example code below. All I have done is replace focus.db with your .db datafiles. It looks like what is happening is that the finemapping isn't finding any place to finemap. Any guidance is appreciated. Is there a change I should make to this line of code?

When I run the command: python \Users\ashatoum\AppData\Local\anaconda3\envs\ma-focus\Scripts\focus finemap OOD_Eur_FOCUS.sumstats.gz:OOD_AA_FOCUS.sumstats.gz 1000G_EUR_Phase3_plink\1000G.EUR.QC.6:split_by_chromosome\g1000_afr_chr6 cortex-EUR_predixcan.db:cortex-AFR_predixcan.db --locations 38:EUR-AFR --chr 6 --out Chromosome_6_OOD_Cor

Thanks,

Alexander

qltanGS commented 5 days ago

Hi Alexander,

The uploaded db files were prepared for PrediXcan method. You should convert them to FOCUS format using FOCUS or MA-FOCUS.

Best, ql

AlexHatoum commented 5 days ago

Hello!

Thanks for the advice. When I do that, the files the converted files are blank. Would you be willing to share the FOCUS files or the code you used to do that?

Thanks,

Alexander