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czbiohub-sf / tabula-muris-senis

Tabula Muris Senis
http://tabula-muris-senis.ds.czbiohub.org
BSD 3-Clause "New" or "Revised" License
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Are the bam files missing for some cells of the FACS data? What are the 'TK' parameters? #45

Closed GexinLiu closed 1 year ago

GexinLiu commented 1 year ago

Hello!

I have downloaded the whole FACS data, but I met a little problem. In the paper, I noticed that there should be 110824 cells sequenced for FACS. When I sorted out all the bam files according to the provided 'tabula-muris-senis-full-metadata.csv' file, I got a total of 106273 bam files and I didn't find those missing bam files in the AWS database.

Another question is that I found a part of fastq.gz files of these missing cell files. So, I want to generate bam files using these fastq.gz files. I noticed that you used STAR v.2.5.2b with parameters TK. Can you tell me what the 'TK parameters' mean since I didn't find them in the STAR?

Thank you very much!

aopisco commented 1 year ago

hi @libraryies the code used is here

unfortunately I won't be able to help further locating the files

GexinLiu commented 1 year ago

OK, thanks for your reply.