frietzelabuvm / ssvqc Goto Github PK

Hi -

Does "0" on the x-axis of the signal heatmaps correspond to peak summit or peak center (or TSS)?

Thanks!

Hi,

do you have config files templates and/or a format description ?

Thanks

Hi,
How do I set up read_mode to bam_PE please?
Cheers!

Hi,

I am new using the tool and I was following the description on the main page using

path <- "/ATAC-PBAF/AK62/Data/QC"
peaks_files <- dir(path, pattern = ".broadPeak", full.names = TRUE)
bw_files <- dir(path, pattern = ".bw$", full.names = TRUE)

Then when I try to run

# Create ssvQC object 
options(mc.cores = 4)
sqc = ssvQC(np_files, bw_files)
sqc = ssvQC.runAll(sqc)

I got the following message

Error in names(cols) <- group_names : 
  'names' attribute [15] must be the same length as the vector [8]

More info about the input files

head (broakPeak)
	3067110	3067542	AK62_Ar_1_REP1.mLb.clN_peak_1	63	.	4.78408	8.36646	6.38689
1	3183757	3184089	AK62_Ar_1_REP1.mLb.clN_peak_2	35	.	3.67095	5.42779	3.56175

> length(peaks_files)
[1] 15

> length(bw_files)
[1] 15

Any advise?

Thanks!

Hi @ssvQC,
I am trying to run ssvQC on my Cut&Run files and I am getting this error:

Error in quantile.default(frip_dt$frip, c(0.1, 0.96)) :
missing values and NaN's not allowed if 'na.rm' is FALSE

Is there a way to set na.rm=TRUE while running the package?

Thank you