phenotype_group assertion error

[ddpinto]

phenotype_group assertion error

[francois-a]

Hi,

Please see this wrapper to see how the files should be formatted and sorted (the format for FastQTL/tensorQTL is the same):
https://github.com/broadinstitute/gtex-pipeline/blob/master/qtl/leafcutter/src/cluster_prepare_fastqtl.py

This needs to be better documented and I'll add a standalone version to this repository. Thanks for pointing it out!

[ddpinto]

Thanks, I've formatted the input accordingly, and the phenotype_group analysis now runs without issues after setting the coordinate for each intron to the TSS of the gene it maps to.

In a related question I wonder if you could comment on the coordinates to use when running tensorQTL on leafcutter introns without phenotype_groups. For the equivalent fastQTL analysis I typically provide the intron-start and intron-end coordinates as input in the bedfile. However, tensorQTL expects a single-base coordinates (where end = start+1). I've considered using the intron mid-point as a proxy but I wonder if it is possible to mimic the fastQTL approach of using the complete intron region instead (i.e. centered on the full intron)?

[zhangpicb]

Hi @francois-a

I use https://github.com/broadinstitute/gtex-pipeline/blob/master/qtl/leafcutter/src/cluster_prepare_fastqtl.py output phenotype_group ,but still get 'Groups defined in input do not match phenotype file (check sort order).

leafcutter.phenotype_groups.txt looks like

chr1:17055:17606:clu_4_-:ENSG00000227232.5      ENSG00000227232.5
chr1:17055:17233:clu_4_-:ENSG00000227232.5      ENSG00000227232.5
chr1:17368:17606:clu_4_-:ENSG00000227232.5      ENSG00000227232.5
chr1:17055:17915:clu_4_-:ENSG00000227232.5      ENSG00000227232.5
chr1:17742:17915:clu_4_-:ENSG00000227232.5      ENSG00000227232.5
chr1:18366:24738:clu_5_-:ENSG00000227232.5      ENSG00000227232.5
chr1:16765:16858:clu_21_-:ENSG00000227232.5     ENSG00000227232.5
chr1:15947:16607:clu_20_-:ENSG00000227232.5     ENSG00000227232.5
chr1:495049:497109:clu_6_-:ENSG00000239906.1    ENSG00000239906.1

leafcutter.bed.gz looks like

#chr    start   end     ID      EP01    EP02
chr1    29569   29570   chr1:17055:17606:clu_4_-:ENSG00000227232.5      0.9728448646222656      -0.6436624661405189
chr1    29569   29570   chr1:17055:17233:clu_4_-:ENSG00000227232.5      -0.3398869558227139     0.16595345366554864
chr1    29569   29570   chr1:17368:17606:clu_4_-:ENSG00000227232.5      -0.10604641028690409    0.38290377873207204
chr1    29569   29570   chr1:17055:17915:clu_4_-:ENSG00000227232.5      1.0070764565362778      -1.1825607021977453
chr1    29569   29570   chr1:17742:17915:clu_4_-:ENSG00000227232.5      -0.47132492764348966    -0.4698074437133793
chr1    29569   29570   chr1:18366:24738:clu_5_-:ENSG00000227232.5      0.07113184542813797     0.6983021090538163
chr1    29569   29570   chr1:16765:16858:clu_21_-:ENSG00000227232.5     0.8037980146700746      0.4932037806525865
chr1    29569   29570   chr1:15947:16607:clu_20_-:ENSG00000227232.5     0.0840760379764529      0.04758884271101856
chr1    140338  140339  chr1:495049:497109:clu_6_-:ENSG00000239906.1    -1.3746907828020156     -1.1099506748505505

Thanks in advanced!