All Perl, Python, R, and Bash Shell scripts were used to eQTLs and RNA-m6A QTLs analysis by integrating QTLtools and MASH.
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Quantify reads density from ChIP-seq or MeRIP-seq data by
1a_QTLtools_quan.peaks.pl
, or quantify gene expression level from RNA-seq data by1b_QTLtools_quan.gene.pl
.QTLtools quan
is invoked in line 125, GTF file may need to be changed based on your file name. More details please seeperl 1a_QTLtools_quan.peaks.pl -help
orperl 1b_QTLtools_quan.gene.pl -help
. -
Get value log2((FPKM_IP+1)/(FPKM_INPUT+1)) of each peak for each MeRIP-seq sample by
2a_log2ratio.peaks.pl
. And get value log2(TPM_INPUT+1) of each gene for each RNA-seq sample (Input of MeRIP-seq) by2b_log2TPM.gene.pl
. More details please seeperl xxx.pl -help
. -
Merge all files from each sample into one file to satisfy the input format of
QTLtools cis
andQTLtools trans
by3a_merge.peaks.pl
or3b_merge.gene.pl
. Please ensure that the colomn orders of the GFT file and the merged file are the same. More details please seeperl xxx.pl -help
. -
Further filter m6A-epaks or genes by
4a_keptRegions.peaks.R
or4b_keptRegions.gene.R
. We can remove peaks or genes with low reads desnity or low variance. More details please see code of4a_keptRegions.peaks.R
or4b_keptRegions.gene.R
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PCA for genotype by
5_QTLtools_pca.SNP.sh
. PCA and PEER factor analysis for phenotype please see the codes under foldercovariates
.
6-8. Identify cis- or trans-QTLs by invoking QTLtools cis
or QTLtools trans
.