SNEEP result files

The resulting files are either provided in the user-specified directory or as defaults in SNEEP_output/.

Main result file (result.txt)

The file lists all the SNPs that cause a significant change in the binding score for a TF (sorted in reserve order, the smallest p-value is listed as the last entry). A single SNP can affect multiple TFs, which results in multiple lines in this file. The first 14 entries are the following:

  • SNP_position chr:start-end (0-based),

  • var1 e.g., effector allele or alternative allele,

  • var2 e.g., wild type allele,

  • rsID

  • MAF

  • peakPosition if an additional footprint/open chromatin region file is used (flag -f), the position of the overlapping region is given; otherwise . (meaning the option was not used).

  • TF name of the affected TF

  • TF-binding_position genomic region, which is bound by the affected TF

  • strand strand to which the TF binds (r) -> reverse strand, (f) -> forward

  • effectedPositionInMotif position within the TF binding motif, which is affected by the SNP

  • pvalue_BindAff_var1 p-value of the binding affinity for var1

  • pvalue_BindAff_var2 p-value of the binding affinity for var2

  • log_pvalueBindAffVar1_pvalueBindAffVar2 logarithmic ratio of the p-value for the binding score of var1 to the p-value for the binding score of var2

  • pvalue_DiffBindAff corresponding p-value for the previous entry (log_pvalueBindAffVar1_pvalueBindAffVar2)

  • fdr_corrected_pvalue FDR corrected p-value for pvalue_DiffBindAff

If the current SNPs overlap with an epigenetic interaction, the following entries, provide more information about the interaction regions. Otherwise, the remaining entries are filled with ‘.’.

  • REM_positions genomic region of the epigentic interaction

  • ensemblIDs ensemble ID of the associated gene

  • geneNames gene name of the associated gene

  • REMIds unique identifier of the epigenetic interactions (if it is an identifier for a REM, it can be used to search for the region in our EpiRegio database)

The last 8 entries contain information specific to EpiRegio. For more information, please have a look at epiregio.de.

Info file (info.txt)

The file info.txt holds the input parameters used for the SNEEP run.

Results of the random background sampling

The results for the random background sampling can be found in the directory sampling and include the randomly sampled SNPs (random_SNPs_<round>.txt) and the randomResult.txt file (format similar to result.txt).