Output Report (-o)

The output report is saved to the user-provided output directory in a file named based on the input FASTQ files (/path/to/output/XXXXX_R1-ID.tab).

Example 1

Below is a sample report based on the results from running EpitopeID on the ENCFF415CJF sample from ENCODE.

EpitopeID   EpitopeCount
LAP-tag 435

GeneID  EpitopeID   EpitopeLocation EpitopeCount    pVal
NR4A1|chr12:52416616-52453291   LAP-tag C-term  9   3.580493355965414e-24

The first part of the report shows which epitopes in Tag_DB were identified in the sample (EpitopeID column) and how many reads mapped to this epitope (EpitopeCount) to help quantify the coverage of the epitopes which relates to the confidence of the call.

The second part of the report shows which epitopes localized to which regions/tiles of the genome significantly (sorted by pvalue if multiple hits). The columns specify the coordinate interval (GeneID), which epitope maps to this locus (EpitopeID), if this occurs on the N or C-terminus (EpitopeLocation), the number of reads mapping to this tile (EpitopeCount), and the poisson-calculated associated p-value to indicate confidence of the site (pVal).

In this report there were 435 reads that mapped to the LAP-tag epitope. The high read count supports "the epitope was successfully integrated into the sample.""

In this report there were 9 read pairs that spanned both the LAP-tag and the NR4A1 gene(at genomic locus chr12:52416616-52453291) toward the sequence encoding the C-terminus. This entry supports that the LAP-tag epitope was integrated at the C-terminus of NF4A1.