Using Tabix to download region of interest from eQTL catalogue

Question

[v.johnson]

I am trying to download a region for colocalisation from the eQTL catalogue uing tabix in R but having no success. Wonder if anyone can help were I am going wrong?

````` fileName = system.file("ftp://ftp.ebi.ac.uk/pub/databases/spot/eQTL/csv/BLUEPRINT/ge/BLUEPRINT_ge_monocyte.all.tsv.gz", package = "seqminer") snp <- tabix.read.table(fileName, "20:46120612-46120613")

also tried:

test <- tabix ("ftp://ftp.ebi.ac.uk/pub/databases/spot/eQTL/csv/BLUEPRINT/ge/BLUEPRINT_ge_monocyte.all.tsv.gz" ,20:46120612-46120613)

Answer 1

[cmdcolin]

I think you have the wrong link, it should be ftp://ftp.ebi.ac.uk/pub/databases/spot/eQTL/sumstats/BLUEPRINT/ge/BLUEPRINT_SE_ge_monocyte.all.tsv.gz

on the command line this works

tabix ftp://ftp.ebi.ac.uk/pub/databases/spot/eQTL/sumstats/BLUEPRINT/ge/BLUEPRINT_SE_ge_monocyte.all.tsv.gz 20:46120612-46120613 
# or equivalent with https, as pierre mentioned
tabix https://ftp.ebi.ac.uk/pub/databases/spot/eQTL/sumstats/BLUEPRINT/ge/BLUEPRINT_SE_ge_monocyte.all.tsv.gz 20:46120612-46120613 

Browse file index here https://ftp.ebi.ac.uk/pub/databases/spot/eQTL/sumstats/BLUEPRINT/ge/

Answer 2

[Pierre Lindenbaum]

tabix doesn't work with the FTP protocolThe protocol + server must support the Range Http Header. https://developer.mozilla.org/en-US/docs/Web/HTTP/Headers/Range

try to replace ftp://ftp with https://ftp.. or http://ftp.. . But It will work only if the server supports those http* protocols.

[cmdcolin]

this is actually not true, tabix works with ftp! this command works on the command line tabix ftp://ftp.ebi.ac.uk/pub/databases/spot/eQTL/sumstats/BLUEPRINT/ge/BLUEPRINT_SE_ge_monocyte.all.tsv.gz 20:46120612-46120613

[Pierre Lindenbaum]

@cmdcolin this is new to me !! thanks !

[Pierre Lindenbaum]

it doesn't work on my side but it may be a proxy problem.

 tabix ftp://ftp.ebi.ac.uk/pub/databases/spot/eQTL/sumstats/BLUEPRINT/ge/BLUEPRINT_SE_ge_monocyte.all.tsv.gz 20:46120612-46120613
[E::hts_itr_next] Failed to seek to offset 89436863228033: Illegal seek
Reading "ftp://ftp.ebi.ac.uk/pub/databases/spot/eQTL/sumstats/BLUEPRINT/ge/BLUEPRINT_SE_ge_monocyte.all.tsv.gz" failed: Illegal seek

[cmdcolin]

I am using samtools/tabix 1.15 for reference in case version affects it