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Not matching barcodes #3

Closed joonan30 closed 1 year ago

joonan30 commented 1 year ago

Dear Charles,

Thanks for the wonderful dataset. It would be very useful resource for the community. I have downloaded the dataset from Google Bucket and GEO. So basically, get the barcodes you used for the processed data and match them with raw files.

When I used the Processed_data_ATAC_BCs-meta-data.csv file, it does not have matching barcodes for the fragment file from the GEO. For example, "ACCACAACATACAGCT-RL2103_ga22_v3" is in the ATAC processed barcode file. But RL2103 is scRNA.... This line has rowname RL1784#TTGCGGGCATTGCGAT-1 - RL1784 is also not valid sample. Can you fix this file?

Another question is that I wanted to get the filtered barcodes you used. It seems that in the "GSM5138510_XXX_snATAC_singlecell.csv.gz" file, you put the column, "cell_id" where some cells have id but others have only "None". I think the cells with cell id are filtered barcodes. Is this correct?

Cheers,

herrinca commented 1 year ago

Apologies for not replying in a timely mannor, we have just returned from our holiday break today.

Thank you for your kind words and for making us aware of this issue. I can not seem to find Processed_data_ATAC_BCs-meta-data.csv, can you point me to where you downloaded it from?

You are correct cell_id "None" refers to filtered barcodes.

Thanks again, Chuck

joonan30 commented 1 year ago

Thanks Chuck,

Processed_data_ATAC_BCs-meta-data.csv is from Google Bucket from here

Downloading the file by console converted the file name like above..

By the way, in the mean time, I dig your code and it seems pretty similar result as you got.

Thanks

herrinca commented 1 year ago

Nice! Good to hear the code works outside of our hands.

Oh ok. I should have pieced together that was the file, haha.

I had a look back through that file and could only find RL2103_ga22_v3 listed in the "predictedCell" column, which is the closest matching snRNA-seq barcode to an ATAC barcode. Please let me know if I overlooked it listed as an ATAC barcode.

RL1784 is our 2yr ATAC sample, so it should be a valid ID. Are you using another source to cross-reference the ATAC sample IDs?

Best