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)
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v.johnson •
2 answers
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/
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 new to me !! thanks !
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
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