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HYsxe / PRINT

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Missing file in BMMCVignette #1

Closed smorabit closed 1 year ago

smorabit commented 1 year ago

Hi Yan,

First of all what an exciting new method for TF analysis!

I was trying to go through the BMMCVignette, and I encountered a problem with a missing data file pretty early in the vignette.

On this line, 

regionsBed <- read.table(paste0(projectDataDir, "BMMCTutorialRegions.bed"))

where projectDataDir = "../../data/BMMCTutorial/"

It seems like in the data folder there is not a directory called BMMCTutorial, and I don't see the .bed file in any of the other folders. Hopefully a simple fix if you could add the missing file.

Thanks, Sam

clip78 commented 1 year ago

Hi,

I was also going through the tutorial and noticed that the "precomputedTn5Bias" folder is not in "data/shared" that should contain the "predBias.rds" file. Looks like an interesting approach for footprinting!

Thanks, Clay

HYsxe commented 1 year ago

Hi! Thanks for the question!

I just uploaded the tutorial data. Could you see if you can access them now?

HYsxe commented 1 year ago

So the predBias.rds is computed for each new data set using the getPrecomputedBias function in the tutorial. To run this function, you need to download the pre-computed bias files from https://zenodo.org/record/7121027#.ZCbw4uzMI8N and put it in the data/shared/precomputedTn5Bias folder. Could you try that and let me know if you run into any issues? Thanks!

clip78 commented 1 year ago

Yes, I see the BMMC tutorial files. OK, I understand now about the predBias file now. I'm downloading the hg38 bias file and will try it out. Thanks for your help!

clip78 commented 1 year ago

The tutorial code seems to be working fine now. I found one issue that the "BMMCTutorialRegions.bed" file did not have a header, so the the read.table function created V1:V3 colnames. The next command creating the granges object, used "chr", "start", and "end" for the colnames. After fixing that and getting a few packages installed, it was working until I got to the pseudobulk files. I can't seem to find the "pseudobulkATAC.rds" or "pseudobulkRNA.rds" files.

HYsxe commented 1 year ago

Those files are a bit big and can't be uploaded to github. I just put them on our zenodo repo at https://zenodo.org/record/7790194#.ZCdmP-zMJTY. It's the BMMCTutorial.tar.gz file. Could you give it a try?

Thanks!

clip78 commented 1 year ago

Great. Yes, I got the files and was able to complete the rest of the tutorial. Thanks for your help. Excited to try this on my data now, but I think this issue can be closed.

Cheers

HYsxe commented 1 year ago

Good to know! Hope our work is helpful for you : )