BioWardrobe ATDP BioWardrobe atdp
The software is used to calculate average tag density profile around all annotated TSS. Such data can be used to estimate the success of ChIP-Seq type experiments for some histone modifications (e.g. H3K4me)
atdp [options] --in=pathToFile --a=pathtoFile --out=pathToFile
| Option | Type | Info |
|---|---|---|
| --in | Required | Input BAM file, bam |
| --out | Required | Base output file name, tsv |
| --a | Required | Annotation file, tsv |
| --log | Optional | Log filename [./logfile_def.log] |
| --index | Optional | Input index BAI file, bai |
| --sam_twicechr | Optional | Which chromosome to double, str |
| --sam_ignorechr | Optional | Which chromosome to ignore, str |
| --f | Optional | Fragmentsize, int [150] |
| --avd_window | Optional | Average tag density window, int [5000] |
| --avd_smooth | Optional | Average smooth window (odd), int [0] |
| --avd_heat_window | Optional | Average tag density window for heatmap, int [10] |