search

dhkron / PSYCHIC

Code for finding putative enhancers using Hi-C data
25 stars 8 forks source link

Annotation of output file #3

Open skytguuu opened 6 years ago

skytguuu commented 6 years ago

Hi, I am interested in your developed tool "PSYCHIC". However, I am confused about this output files. According to your description, I checked ".enh_p.bed" file. It seems the output is as followed: ############### chr20 1320000 1360000 RAD21L1:120Kb:0.0027:5.6e-05:21:45 chr20 1360000 1400000 RAD21L1:160Kb:0.0036:0.00015:16:39 ############### my question is, is chr20:1320000-1360000 the TAD domain? What is the last few columns followed the gene "RAD21L1"? (like 120kb? 0.0027:5.6e-0.5:21:45) Another question is about ".model.estimated.params.bed" file. The output is: ############################### chr20 0 1360000 TAD -0.8656 18.9715 0.9231 NaN NaN NaN 20.3321 chr20 1400000 2520000 TAD -0.5036 12.7112 0.9702 -1.0690 23.1316 0.9098 17.6652 ############################### I still did not understand your description about this file? Such as (-0.8655,18.9715...) Could you give me some help? Thanks

dhkron commented 6 years ago

Hello!

For your first question, you may find the output formats in here and here. In any case, the output format for the enhancer files is - chromsome, predicted enhancer start, predicted enhancer end, gene name, distance between predicted enhancer and gene, FDR corrected value, P-value, Hi-C fit, Hi-C data

For the second question - format is here at BedWrite - chromosome, region start, region end, region type (TAD/Merge/Sky), [rest are power law/bilinear power law estimators]