swaruplab/Single-nuclei-epigenomic-and-transcriptomic-landscape-in-Alzheimer-disease

Fragment file availablity

Biocard opened this issue · 1 comments

Biocard commented

I would like to start by expressing my gratitude for all the support and contributions made on this platform.

I am reaching out to request assistance regarding the code "snATAC_processing.R" on Github. Specifically, I am interested in the 18th line of this code which references the file "fragment.path <- "cellranger_aggr/outs/fragments.tsv.gz"". It appears that this fragment file is a result of integrating various AD sample fragment files. However, this file has not been uploaded to GSE174367.

Moreover, it seems that the fragment file is available on https://www.synapse.org/#!Synapse:syn22079621/, but it requires "Download Permission". Unfortunately, I do not have access to this permission, and thus, I am unable to obtain this important file.

Would anyone kindly provide me with this missing fragment file? Your help and support are highly appreciated.

Thank you once again for your valuable time and effort.

smorabit commented

Hi,

If you don't have access to synapse, to generate the fragments file you can download the sequencing data from SRA and then run cellrangeratac to generate the fragments file.