Cannot use the GSE123576_mousebrain_countsData_revision.csv.gz in GEO

[genecell]

Hi,

Very useful resource!
I cannot open the Cannot use the GSE123576_mousebrain_countsData_revision.csv.gz in GEO: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE123576.
I got the following error message, and also cannot import the data in R:

gunzip -c GSE123576_mousebrain_countsData_revision.csv.gz > GSE123576_mousebrain_countsData_revision.csv
gzip: GSE123576_mousebrain_countsData_revision.csv.gz: invalid compressed data--format violated

Could you please provide some suggestions to solve the above problem?
Thank you!

[caleblareau]

Hm— this is strange. I know of several others that have used the dataset successfully. I just verified it myself as well. Maybe your download was incomplete? ``` (base) clareau@ganapati:~$wget ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123576/suppl/GSE123576_mousebrain_countsData_revision.csv.gz (base) clareau@ganapati:~$ gunzip -c GSE123576_mousebrain_countsData_revision.csv.gz > GSE123576_mousebrain_countsData_revision.csv (base) clareau@ganapati:~$ head GSE123576_mousebrain_countsData_revision.csv peak_idx cell_idx count 8 1 1 17 1 1 41 1 1 89 1 1 98 1 1 142 1 1 161 1 2 162 1 1 ``` On Jan 23, 2021, at 10:45 PM, Min Dai <[email protected]<mailto:[email protected]>> wrote: Hi, Very useful resource! I cannot open the Cannot use the GSE123576_mousebrain_countsData_revision.csv.gz in GEO: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE123576. I got the following error message, and also cannot import the data in R: gunzip -c GSE123576_mousebrain_countsData_revision.csv.gz > GSE123576_mousebrain_countsData_revision.csv gzip: GSE123576_mousebrain_countsData_revision.csv.gz: invalid compressed data--format violated Could you please provide some suggestions to solve the above problem? Thank you! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub<#2>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AD32FYLWSMW4MZAKXG6AMIDS3O6YRANCNFSM4WQJPDDA>.

[genecell]

Hm— this is strange. I know of several others that have used the dataset successfully. I just verified it myself as well. Maybe your download was incomplete? (base) clareau@ganapati:~$wget [ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123576/suppl/GSE123576_mousebrain_countsData_revision.csv.gz](ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123576/suppl/GSE123576_mousebrain_countsData_revision.csv.gz) (base) clareau@ganapati:~$ gunzip -c GSE123576_mousebrain_countsData_revision.csv.gz > GSE123576_mousebrain_countsData_revision.csv (base) clareau@ganapati:~$ head GSE123576_mousebrain_countsData_revision.csv peak_idx cell_idx count 8 1 1 17 1 1 41 1 1 89 1 1 98 1 1 142 1 1 161 1 2 162 1 1 On Jan 23, 2021, at 10:45 PM, Min Dai <[email protected]mailto:[email protected]> wrote: Hi, Very useful resource! I cannot open the Cannot use the GSE123576_mousebrain_countsData_revision.csv.gz in GEO: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE123576. I got the following error message, and also cannot import the data in R: gunzip -c GSE123576_mousebrain_countsData_revision.csv.gz > GSE123576_mousebrain_countsData_revision.csv gzip: GSE123576_mousebrain_countsData_revision.csv.gz: invalid compressed data--format violated Could you please provide some suggestions to solve the above problem? Thank you! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub<#2>, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AD32FYLWSMW4MZAKXG6AMIDS3O6YRANCNFSM4WQJPDDA.

Thank you for your rapid reply, I'll download it again and I think the error is just on my side.
Thanks!