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guanjue / IDEAS_2018

Jointly characterizing epigenetic dynamics across multiple cell types
MIT License
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IDEAS not finishing #9

Closed aidanmacnamara closed 5 years ago

aidanmacnamara commented 5 years ago

Hi there,

I've been trying to test IDEAS using some bigWig files. I've looked at 2 samples with 5 marks each - the code seems to run okay but I get the message that "IDEAS didn't finish within 3 days". I'll start digging into this error but is there anything obvious I should check?

Many thanks.

guanjue commented 5 years ago

The IDEAS does not use bigiwig file as input file. You need to convert the bigwig file into the signal file. The signal is just one column of the signal of each bin on your genome. You can get that by using the ucsc bigWigAverageOverBed utility

cell_mark=NK_atac bigWigAverageOverBed $cell_mark'.bw' whole_genome_bin.bed $cell_mark'.bw.tab' sort -k1,1 $cell_mark'.bw.tab' | cut -f5 > $cell_mark'.bw.tab.sig'

We are currently setting up a new pipeline of IDEAS using bigwig as input.

Guanjue

aidanmacnamara commented 5 years ago

Thanks Guanjue, I'll try that.