Based on BioWardrobe iaintersect
The software assigns each peak obtained from MACS2 to a gene and region (upstream, promoter, exon, intron, intergenic).
iaintersect [options] --in=pathToFile --a=pathtoFile --out=pathToFile
| Option | Type | Info |
|---|---|---|
| --in | Required | Input filename with MACS2 peak calling results, xls |
| --out | Required | Base output file name, tsv |
| --a | Required | Annotation file, tsv |
| --log | Optional | Log filename (default ./logfile_def.log) |
| --promoter | Optional | Promoter region around TSS, base pairs |
| --upstream | Optional | Upstream region before promoter, base pairs |
| --sam_ignorechr | Optional | The chromosome to be ignored, string |