eQTL Catalogue Browser: limitation

Question

[Shicheng Guo]

Hi All,

I am trying to use eQTL Catalogue Browser and want to know is there any limitation for this database?

https://elixir.ut.ee/eqtl/

Thanks.

Shicheng

Answer 1

[jared.andrews07]

Assuming you mean use-restriction, rather than any inherent biological limitations of eQTLs, the data contained within said database, etc, then no, not really. The data itself has a creative commons license, as stated here, so you can basically do whatever you want with it so long as you give credit.

Answer 2

[Shicheng Guo]

Thanks Andrews: I downloaded the data and find the 1st and 2nd column are not chr and pos, is there any easy way to perform tabix index to these data? I don't want to manually remove the 1st column since there are 250 files overall and each of them are very large.

molecular_trait_id      chromosome      position        ref     alt     variant ma_samples      maf     pvalue  beta    se      type    ac      an      r2      molecular_trait_object_id       gene_id median_tpm      rsid
ENST00000246421 1       1027340 C       T       chr1_1027340_C_T        29      0.074359        0.287106        -0.291019       0.272582        SNP     26      390     0.44585 ENSG00000215790 ENSG00000215790 7.9     rs28670633
ENST00000263741 1       1027340 C       T       chr1_1027340_C_T        29      0.074359        0.806176        0.0690052       0.280826        SNP     26      390     0.44585 ENSG00000078808 ENSG00000078808 81.434  rs28670633
ENST00000291386 1       1027340 C       T       chr1_1027340_C_T        29      0.074359        0.68728 -0.0465225      0.115384        SNP     26      390     0.44585 ENSG00000160075 ENSG00000160075 54.001  rs28670633
ENST00000304952 1       1027340 C       T       chr1_1027340_C_T        29      0.074359        0.31759 0.426646        0.425714        SNP     26      390     0.44585 ENSG00000188290 ENSG00000188290 4.314   rs28670633
ENST00000307786 1       1027340 C       T       chr1_1027340_C_T        29      0.074359        0.421041        0.27594 0.342165        SNP     26      390     0.44585 ENSG00000169885 ENSG00000169885 0.559   rs28670633
ENST00000308647 1       1027340 C       T       chr1_1027340_C_T        29      0.074359        0.68206 -0.0704446      0.171684        SNP     26      390     0.44585 ENSG00000160072 ENSG00000160072 9.627   rs28670633
ENST00000309212 1       1027340 C       T       chr1_1027340_C_T        29      0.074359        0.272491        -0.252715       0.229595        SNP     26      390     0.44585 ENSG00000162576 ENSG00000162576 3.863   rs28670633
ENST00000321751 1       1027340 C       T       chr1_1027340_C_T        29      0.074359        0.546649        0.0981196       0.162469        SNP     26      390     0.44585 ENSG00000175756 ENSG00000175756 100.1   rs28670633
ENST00000323275 1       1027340 C       T       chr1_1027340_C_T        29      0.074359        0.0523047       -0.629631       0.322313        SNP     26      390     0.44585 ENSG00000127054 ENSG00000127054 37.72   rs28670633
ENST00000325425 1       1027340 C       T       chr1_1027340_C_T        29      0.074359        0.94527 -0.0214266      0.31169 SNP     26      390     0.44585 ENSG00000162572 ENSG00000162572 4.635   rs28670633
ENST00000327044 1       1027340 C       T       chr1_1027340_C_T        29      0.074359        0.374507        0.20981 0.235672        SNP     26      390     0.44585 ENSG00000188976 ENSG00000188976 25.454  rs28670633
ENST00000328596 1       1027340 C       T       chr1_1027340_C_T        29      0.074359        0.100083        0.45372 0.274498        SNP     26    

Tried -S and -b, but received another error: [E::hts_idx_push] Chromosome blocks not continuous

(base) [sguo2@login02 eqtlcatalog]$ tabix -b 2 -S 1 -p vcf Quach_2016_exon_monocyte_R848.all.tsv.gz
[E::hts_idx_push] Chromosome blocks not continuous
tbx_index_build failed: Quach_2016_exon_monocyte_R848.all.tsv.gz
(base) [sguo2@login02 eqtlcatalog]$ less Quach_2016_tx_monocyte_R848.all.tsv.gz