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rr1859 / R.4Cker

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nbanalysis error, seq.default #53

Closed Inswasti closed 6 years ago

Inswasti commented 6 years ago

Hello Ramya,

Would you help me with the nearBaitAnalysis error that I've got? I ran this: nb_mir_pass <- nearBaitAnalysis(mir_pass,k=5)

and got this output: [1] "Building adaptive windows..." [1] "Normalizing counts..." [1] "Generating synthetic samples...." Error in seq.default(1, (num_windows - 32), by = 30) : wrong sign in 'by' argument

The code to produce the 4C-ker object (I tested with files that passed QC) is: mir_pass = createR4CkerObjectFromFiles(files = c("HOT-MIR_outputs/P1_merged/MIR335_P1_merged.bedGraph", "HOT-MIR_outputs/P2/MIR335_P2.bg", "HOT-MIR_outputs/P3/MIR335_P3.bedGraph", "HOT-MIR_outputs/P4/MIR335_P4.bedGraph", "HOT-MIR_outputs/P5/MIR335_P5.bedGraph", "HOT-MIR_outputs/P6/MIR335_P6.bedGraph"), bait_chr = "chr7", bait_coord = 130497245, bait_name = "MIR335", primary_enz = "CCGG", samples = c("p1", "p2","p3","p4","p5","p6"), conditions = c("WT","patient"), replicates = c(3,3), species = "hs", output_dir = "R_project/4C_MIR335/2018_08_20_4cker_05", enz_file = enz_file)

Tried to search for similar issues in this forum, couldn't find it. Thanks a lot for your help :)

Inswasti commented 6 years ago

I think I sorted this by cleaning my .bedGraph file from the non-standard chromosome coordinates (e.g. _alt, chrUn, etc.) and subtracting the adjacent window coordinates of the bait. Then, I played with different k values, for my data.

My data needs tweaking before I can feed it to the 4C-ker pipeline because the upstream procedure is rather different, with only using one 4bp-cutter enzyme to prepare the library. Also, some fragmentation of the PCR products before sequencing.